Predicting the impacts of climate change on genetic diversity in an endangered lizard species

Many endangered species persist as a series of isolated populations, with some populations more genetically diverse than others. If climate change disproportionately threatens the most diverse populations, the species' ability to adapt (and hence its long-term viability) may be affected more severely than would be apparent by its numerical reduction. In the present study, we combine genetic data with modelling of species distributions under climate change to document this situation in an endangered lizard (Eulamprus leuraensis) from montane southeastern Australia. The species is known from only about 40 isolated swamps. Genetic diversity of lizard populations is greater in some sites than others, presumably reflecting consistently high habitat suitability over evolutionary time. Species distribution modelling suggests that the most genetically diverse populations are the ones most at risk from climate change, so that global warming will erode the species' genetic variability faster than it curtails the species' geographic distributio

Physicochemical space of synthetic and natural pesticides – a meta-analysis

The first commercial use of synthetic pesticides for crop protection dates back to the 1940s, followed by a fast spreading of their use and the development of a large number of compounds. In contrast to synthetic pesticides that are nowadays designed with the help of artificial intelligence that includes computational science and combinatorial chemistry, natural pesticides are the results of long evolutionary processes involving specific host-pathogens, predator-prey and competitor interactions. For these reasons, natural pesticides are often more specific and less harmful to the environment. Natural pesticides are very diverse and can be found in various living organisms. In the present study, we investigated differences in the physicochemical space occupied by synthetic and natural pesticides. In this respect, we measured the mean and breadth of synthetic and natural pesticides, as well as the overlap between these groups in a reduced physicochemical space derived from a set of 44 physicochemical variables. We showed that physicochemical space strongly differs between synthetic and natural pesticides and could be determined with 93-100% certainty, a result comparable to differences observed in drugs. Importantly, the physicochemical space occupied by synthetic pesticides was 2.6 fold smaller than the one of natural pesticides and toxicity potential was lower in the latter. In conclusion, our work showed that the design of commercialized synthetic pesticides is underexploiting the possible physicochemical space of known natural pesticides, likely due to specific constraints. Such limitations should trigger the development of efficient natural pesticides avoiding as much as possible detrimental effects on non-target organism

Cytogenetic and Molecular Relationships between Zarudny'S Rock Shrew (Crocidura zarudnyi; Mammalia: Soricomorpha) and Eurasian Taxa

We karyotyped and sequenced 1,140 base pairs of the mitochondrial DNA cytochrome b of a specimen of Zarudny's rock shrew (Crocidura zarudnyi) from Baluchestan, southeastern Iran, to clarify its cytogenetic and molecular relationships with other Eurasian species of Crocidura. According to the karyotype (2N = 40, FN = 50), Zarudny's rock shrew belongs to the group of the lesser white-toothed shrew (C. suaveolens), which is different from other known crocidurine karyotypes, considering the combination of the diploid and fundamental number of chromosomes. Molecular results revealed that C. zarudnyi is included in a monophyletic clade with the C. suaveolens group, where it is a sister taxon to the others (mean Kimura 2-parameter distance = 9.7%

Multiple uprising invasions of Pelophylax water frogs, potentially inducing a new hybridogenetic complex

peer reviewedThe genetic era has revolutionized our perception of biological invasions. Yet, it is usually too late to understand their genesis for efficient management. Here, we take the rare opportunity to reconstruct the scenario of an uprising invasion of the famous water frogs (Pelophylax) in southern France, through a fine-scale genetic survey. We identified three different taxa over less than 200 km2: the autochthonous P. perezi, along with the alien P. ridibundus and P. kurtmuelleri, which have suddenly become invasive. As a consequence, the latter hybridizes and may now form a novel hybridogenetic complex with P. perezi, which could actively promote its replacement. This exceptional situation makes a textbook application of genetics to early-detect, monitor and understand the onset of biological invasions before they pose a continental-wide threat. It further emphasizes the alarming rate of amphibian translocations, both at global and local scales, as well as the outstanding invasive potential of Pelophylax aliens

Landscape genetics of the Alpine newt ( Mesotriton alpestris ) inferred from a strip-based approach

Habitat destruction and fragmentation are known to strongly affect dispersal by altering the quality of the environment between populations. As a consequence, lower landscape connectivity is expected to enhance extinction risks through a decrease in gene flow and the resulting negative effects of genetic drift, accumulation of deleterious mutations and inbreeding depression. Such phenomena are particularly harmful for amphibian species, characterized by disjunct breeding habitats. The dispersal behaviour of amphibians being poorly understood, it is crucial to develop new tools, allowing us to determine the influence of landscape connectivity on the persistence of populations. In this study, we developed a new landscape genetics approach that aims at identifying land-uses affecting genetic differentiation, without a priori assumptions about associated ecological costs. We surveyed genetic variation at seven microsatellite loci for 19 Alpine newt (Mesotriton alpestris) populations in western Switzerland. Using strips of varying widths that define a dispersal corridor between pairs of populations, we were able to identify land-uses that act as dispersal barriers (i.e. urban areas) and corridors (i.e. forests). Our results suggest that habitat destruction and landscape fragmentation might in the near future affect common species such as M. alpestris. In addition, by identifying relevant landscape variables influencing population structure without unrealistic assumptions about dispersal, our method offers a simple and flexible tool of investigation as an alternative to least-cost models and other approache

Assessment of terrestrial small mammals and a record of the critically endangered shrew Crocidura wimmeri in Banco National Park (Côte d'Ivoire)

This study investigated the small mammal community of the periurban Banco National Park (34 km2), Abidjan, Côte d'Ivoire, using identical numbers of Sherman and Longworth traps. We aimed to determine the diversity and distribution of rodents and shrews in three different habitats: primary forest, secondary forest and swamp. Using 5014 trap-nights, 91 individuals were captured that comprised seven rodent and four shrew species. The trapping success was significantly different for each species, i.e., the Longworth traps captured more soricids (31/36 shrews), whereas the Sherman traps captured more murids (37/55 mice). The most frequent species was Praomys cf. rostratus, followed by Crocidura buettikoferi, Hybomys trivirgatus and Crocidura jouvenetae. Indices of species richness (S) and diversity (H′) were greatest in primary forest, followed by secondary forest and swamp. Several expected species, such as Crocidura obscurior, were not found, whereas we captured four specimens of the critically endangered (IUCN 2012) Wimmer's shrew Crocidura wimmeri, a species that has vanished from its type locality, Adiopodoumé. Therefore, Banco National Park represents an important sanctuary, not only for plants, birds and primates, but also for other small forest vertebrate

Molecular evolution of Azagny virus, a newfound hantavirus harbored by the West African pygmy shrew (Crocidura obscurior) in Côte d'Ivoire

<p>Abstract</p> <p>Background</p> <p>Tanganya virus (TGNV), the only shrew-associated hantavirus reported to date from sub-Saharan Africa, is harbored by the Therese's shrew (<it>Crocidura theresae</it>), and is phylogenetically distinct from Thottapalayam virus (TPMV) in the Asian house shrew (<it>Suncus murinus</it>) and Imjin virus (MJNV) in the Ussuri white-toothed shrew (<it>Crocidura lasiura</it>). The existence of myriad soricid-borne hantaviruses in Eurasia and North America would predict the presence of additional hantaviruses in sub-Saharan Africa, where multiple shrew lineages have evolved and diversified.</p> <p>Methods</p> <p>Lung tissues, collected in RNAlater^®, from 39 Buettikofer's shrews (<it>Crocidura buettikoferi</it>), 5 Jouvenet's shrews (<it>Crocidura jouvenetae</it>), 9 West African pygmy shrews (<it>Crocidura obscurior</it>) and 21 African giant shrews (<it>Crocidura olivieri</it>) captured in Côte d'Ivoire during 2009, were systematically examined for hantavirus RNA by RT-PCR.</p> <p>Results</p> <p>A genetically distinct hantavirus, designated Azagny virus (AZGV), was detected in the West African pygmy shrew. Phylogenetic analysis of the S, M and L segments, using maximum-likelihood and Bayesian methods, under the GTR+I+Γ model of evolution, showed that AZGV shared a common ancestry with TGNV and was more closely related to hantaviruses harbored by soricine shrews than to TPMV and MJNV. That is, AZGV in the West African pygmy shrew, like TGNV in the Therese's shrew, did not form a monophyletic group with TPMV and MJNV, which were deeply divergent and basal to other rodent- and soricomorph-borne hantaviruses. Ancestral distributions of each hantavirus lineage, reconstructed using Mesquite 2.74, suggested that the common ancestor of all hantaviruses was most likely of Eurasian, not African, origin.</p> <p>Conclusions</p> <p>Genome-wide analysis of many more hantaviruses from sub-Saharan Africa are required to better understand how the biogeographic origin and radiation of African shrews might have contributed to, or have resulted from, the evolution of hantaviruses.</p

Genomic Evidence for Cryptic Speciation in Tree Frogs From the Apennine Peninsula, With Description of Hyla perrini sp. nov

Despite increasing appreciation of the speciation continuum, delimiting and describing new species is a major yet necessary challenge of modern phylogeography to help optimize conservation efforts. In amphibians, the lack of phenotypic differences between closely-related taxa, their complex, sometimes unresolved phylogenetic relationships, and their potential to hybridize all act to blur taxonomic boundaries. Here we implement a multi-disciplinary approach to evaluate the nature of two deeply-diverged mitochondrial lineages previously documented in Italian tree frogs (Hyla intermedia s. l.), distributed north and south of the Northern Apennine Mountains. Based on evidence from mitochondrial phylogenetics, nuclear phylogenomics, hybrid zone population genomics, niche modeling analyses, and biometric assessments, we propose that these lineages be considered distinct, cryptic species. Both mitochondrial and nuclear data affirm that they belong to two monophyletic clades of Pliocene divergence (~3.5 My), only admixing over a relatively narrow contact zone restricted to the southeast of the Po Plain (50–100 km). These characteristics are comparable to similarly-studied parapatric amphibians bearing a specific status. Inferred from their current geographic distribution, the two Italian tree frogs feature distinct ecological niches (&lt;15% of niche overlap), raising questions regarding potential adaptive components contributing to their incipient speciation. However, we found no diagnostic morphological and bioacoustic differences between them. This system illustrates the speciation continuum of Western-Palearctic tree frogs and identifies additional cryptic lineages of similar divergence to be treated as separate species (H. cf. meridionalis). We recommend combined approaches using genomic data as applied here for the future taxonomic assessment of cryptic diversity in alloparapatric radiations of terrestrial vertebrates, especially in controversial taxa. Finally, we formally described the northern Italian tree frogs as a new species, Hyla perrini sp. nov

Using Combined Morphological, Allometric and Molecular Approaches to Identify Species of the Genus Raillietiella (Pentastomida)

Taxonomic studies of parasites can be severely compromised if the host species affects parasite morphology; an uncritical analysis might recognize multiple taxa simply because of phenotypically plastic responses of parasite morphology to host physiology. Pentastomids of the genus Raillietiella are endoparasitic crustaceans primarily infecting the respiratory system of carnivorous reptiles, but also recorded from bufonid anurans. The delineation of pentastomids at the generic level is clear, but the taxonomic status of many species is not. We collected raillietiellids from lungs of the invasive cane toad (Rhinella marina), the invasive Asian house gecko (Hemidactylus frenatus), and a native tree frog (Litoria caerulea) in tropical Australia, and employed a combination of genetic analyses, and traditional and novel morphological methods to clarify their identity. Conventional analyses of parasite morphology (which focus on raw values of morphological traits) revealed two discrete clusters in terms of pentastome hook size, implying two different species of pentastomes: one from toads and a tree frog (Raillietiella indica) and another from lizards (Raillietiella frenatus). However, these clusters disappeared in allometric analyses that took pentastome body size into account, suggesting that only a single pentastome taxon may be involved. Our molecular data revealed no genetic differences between parasites in toads versus lizards, confirming that there was only one species: R. frenatus. This pentastome (previously known only from lizards) clearly is also capable of maturing in anurans. Our analyses show that the morphological features used in pentastomid taxonomy change as the parasite transitions through developmental stages in the definitive host. To facilitate valid descriptions of new species of pentastomes, future taxonomic work should include both morphological measurements (incorporating quantitative measures of body size and hook bluntness) and molecular data