Are human-induced changes good or bad to dynamic landscape connectivity?

Land managers must find a compromise between rapidly changing landscapes and biodiversity conservation through ecological networks. Estimating ecological networks is a key approach to enhance or maintain functional connectivity by identifying the nodes and links of a graph, which represent habitats and their corresponding functional corridors, respectively. To understand the current state of biodiversity, it is necessary to consider dynamic landscape connectivity while relying on relevant land cover maps. Although a current land cover map is relatively easy to produce using existing data, this is challenging for past landscapes. Here we investigated the impact of changes in landscape connectivity in an urban landscape at a fine scale on the habitat availability of two bird species: the tree pipit Anthus trivialis and the short-toed treecreeper Certhia brachydactyla. These species, exhibiting different niche ecologies, have shown contrasting population trends at a medium-term scale. The occurrences of C. brachydactyla were better correlated with resistance values that maximise the use of corridors, whereas the occurrences of A. trivialis better fitted with intermediate resistance values. The statistical approach indirectly highlighted relevant information about the ecology the capacity of both species to use urban habitats. Landscape connectivity increased for both species over the 24-year study period and may have implications for local abundances, which could explain, at the national scale, the increase in populations of C. brachydactyla, but not the decrease in populations of A. trivialis. Thus, more attention must be paid on rural habitats and their associated species that are more impacted by human activities, but efforts could also be achieved in urban areas especially for highly corridor-dependent species. Studying dynamic landscape connectivity at a fine scale is essential for estimating past and future land cover changes and their associated impacts on ecological networks, to better reconcile human and biodiversity concerns in land management.

Mapping past land cover on Poitiers in 1993 at very high resolution using GEOBIA approach and open data.

The land cover data presented here is a reconstruction of the past landscape (1993) at Very High Resolution (VHR) for the city of Poitiers, France. This reconstruction is based on multiple sources of images and data. We combined the strengths of both mono-temporal and multi-temporal classifications. Orthophotos were created at a spatial resolution of 0.5 m using aerial raw images from the French National Geographic Institute (IGN), taken during two aerial missions in July and August 1993. These orthophotos were merged at a spatial resolution of 5 m to conduct a first object-based classification using Landsat-5 TM images. The goal was to identify croplands, grasslands, coniferous and deciduous forests, urban areas, water bodies, and shadows. This learning-based classification employed a dataset consisting of 1371 polygons and demonstrated strong classification performances, achieving an overall accuracy of 86.31% and a kappa index of 0.832. On the other hand, mono-temporal classifications at a 0.5 m spatial resolution were carried out on each orthophoto to extract trees and herbaceous vegetation, especially in urban contexts. As mono-temporal classifications contained less information, we used a larger number of polygons for the learning step: 3849 and 5173 polygons for the northern and southern classifications, respectively. The segmentation step performed better in urban areas compared to rural areas. Consequently, the performance of classifications was evaluated separately for both contexts. Urban areas exhibited excellent performances, achieving kappa indices of 0.897 and 0.881 for the northern and southern classifications, respectively, whereas only tree vegetation was accurately detected in rural areas. To compensate for the lack of information such as buildings, railways, or roads, we modified the BD TopoⓇ dataset from IGN. This land cover map provides highly detailed information, facilitating the understanding of urban sprawl and changes in urban and rural vegetation surrounding the city of Poitiers. Due to these reasons, this freely accessible map can be utilized by researchers, land managers, and private companies for addressing urban and ecological challenges.

Heterogeneous distribution of sex ratio distorters in natural populations of the isopod Armadillidium vulgare.

In the isopod Armadillidium vulgare, many females produce progenies with female-biased sex ratios, owing to two feminizing sex ratio distorters (SRD): Wolbachia endosymbionts and the f element. We investigated the distribution and population dynamics of these SRD and mitochondrial DNA variation in 16 populations from Europe and Japan. Confirming and extending results from the 1990s, we found that the SRD are present at variable frequencies in populations and that the f element is overall more frequent than Wolbachia. The two SRD never co-occur at high frequency in any population, suggesting an apparent mutual exclusion. We also detected Wolbachia or the f element in some males, which probably reflects insufficient titer to induce feminization or presence of masculinizing alleles. Our results are consistent with a single integration event of a Wolbachia genome in the A. vulgare genome at the origin of the f element, which contradicts an earlier hypothesis of frequent losses and gains. We identified strong linkage between Wolbachia strains and mitochondrial haplotypes, but no association between the f element and mitochondrial background. Our results open new perspectives on SRD evolutionary dynamics in A. vulgare, the evolution of genetic conflicts and their impact on the variability of sex determination systems.

Hybridization increases genetic diversity in Schistosoma haematobium populations infecting humans in Cameroon.

BACKGROUND: Hybrids between Schistosoma haematobium (Sh) and S. bovis (Sb) have been found in several African countries as well as in Europe. Since the consequences of this hybridization are still unknown, this study aims to verify the presence of such hybrids in Cameroonian humans, to describe the structure of S. haematobium populations on a large geographic scale, and to examine the impact of these hybrids on genetic diversity and structure of these populations. METHODS: From January to April 2019, urine from infected children was collected in ten geographically distinct populations. Miracidia were collected from eggs in this urine. To detect the presence of hybrids among these miracidia we genotyped both Cox1 (RD-PCR) and ITS2 gene (PCR-RFLP). Population genetic diversity and structure was assessed by genotyping each miracidium with a panel of 14 microsatellite markers. Gene diversity was measured using both heterozygosity and allelic richness indexes, and genetic structure was analyzed using paired Fst, PCA and Bayesian approaches. RESULTS: Of the 1327 miracidia studied, 88.7% were identified as pure genotypes of S. haematobium (Sh_Sh/Sh) while the remaining 11.3% were hybrids (7.0% with Sh_Sh/Sb, 3.7% with Sb_Sb/Sh and 0.4% with Sb_Sh/Sb). No miracidium has been identified as a pure genotype of S. bovis. Allelic richness ranged from 5.55 (Loum population) to 7.73 (Matta-Barrage) and differed significantly between populations. Mean heterozygosity ranged from 53.7% (Loum) to 59% (Matta Barrage) with no significant difference. The overall genetic differentiation inferred either by a principal component analysis or by the Bayesian approach shows a partial structure. Southern populations (Loum and Matta Barrage) were clearly separated from other localities but genetic differentiation between northern localities was limited, certainly due to the geographic proximity between these sites. CONCLUSIONS: Hybrids between S. haematobium and S. bovis were identified in 11.3% of miracidia that hatched from eggs present in the urine of Cameroonian schoolchildren. The percentages of these hybrids are correlated with the genetic diversity of the parasite, indicating that hybridization increases genetic diversity in our sampling sites. Hybridization is therefore a major biological process that shapes the genetic diversity of S. haematobium.

Iguanainsularis (Iguanidae) from the southern Lesser Antilles: An endemic lineage endangered by hybridization.

The newly described horned iguanaIguanainsularis from the southern Lesser Antilles is separated in two easily recognized subspecies: I.insularissanctaluciae from St. Lucia and I.insularisinsularis from the Grenadines. Its former description is completed by the use of 38 new samples for genetic and morphological analysis. Seventeen microsatellites were used to estimate genetic diversity, population structure and the level of introgression with other Iguana species over nearly the whole range of the species. ND4 and PAC sequences were also used to better characterize hybridization and to complete the description of this lineage. The I.insularis population of St. Vincent shows a high level of introgression from I.iguana whereas in the Grenadines, most islands present pure insularis populations but several show evidence of introgressions. Of the two remaining populations of I.insularissanctaluciae, only one is still purebred. The recent identification of this and other distinct insular species and subspecies in the eastern Caribbean, and evaluation of where hybridization has occurred, are timely and important because the native iguanas are in urgent need of conservation action. Among the greatest threats is the ongoing human-mediated spread of invasive iguanas from Central and South America, which are destroying the endemic insular lineages through multiple diachronic introgression events.

Experimental evidence of Wolbachia introgressive acquisition between terrestrial isopod subspecies.

Wolbachia are the most widespread endosymbiotic bacteria in animals. In many arthropod host species, they manipulate reproduction via several mechanisms that favor their maternal transmission to offspring. Among them, cytoplasmic incompatibility (CI) promotes the spread of the symbiont by specifically decreasing the fertility of crosses involving infected males and uninfected females, via embryo mortality. These differences in reproductive efficiency may select for the avoidance of incompatible mating, a process called reinforcement, and thus contribute to population divergence. In the terrestrial isopod Porcellio dilatatus, the Wolbachia wPet strain infecting the subspecies P. d. petiti induces unidirectional CI with uninfected individuals of the subspecies P. d. dilatatus. To study the consequences of CI on P. d. dilatatus and P. d. petiti hybridization, mitochondrial haplotypes and Wolbachia infection dynamics, we used population cages seeded with different proportions of the 2 subspecies in which we monitored these genetic parameters 5 and 7 years after the initial setup. Analysis of microsatellite markers allowed evaluating the degree of hybridization between individuals of the 2 subspecies. These markers revealed an increase in P. d. dilatatus nuclear genetic signature in all mixed cages, reflecting an asymmetry in hybridization. Hybridization led to the introgressive acquisition of Wolbachia and mitochondrial haplotype from P. d. petiti into nuclear genomes dominated by alleles of P. d. dilatatus. We discuss these results with regards to Wolbachia effects on their host (CI and putative fitness cost), and to a possible reinforcement that may have led to assortative mating, as possible factors contributing to the observed results.

Genetic evidence for the role of non-human primates as reservoir hosts for human schistosomiasis.

BACKGROUND: Schistosomiasis is a chronic parasitic disease, that affects over 207 million people and causes over 200,000 deaths annually, mainly in sub-Saharan Africa. Although many health measures have been carried out to limit parasite transmission, significant numbers of non-human primates such as Chlorocebus aethiops (Ch. aethiops) (vervet) and Papio anubis (baboon) are infected with S. mansoni, notably in Ethiopia, where they are expected to have potentially significant implications for transmission and control efforts. OBJECTIVE: The objective of this study was to assess and compare the genetic diversity and population structure of S. mansoni isolates from human and non-human primates free-ranging in close proximity to villages in selected endemic areas of Ethiopia. METHODS: A cross-sectional study was conducted in three transmission sites: Bochesa, Kime and Fincha. A total of 2,356 S. mansoni miracidia were directly isolated from fecal specimens of 104 hosts (i.e. 60 human hosts and 44 non-human primates). We performed DNA extraction and PCR amplification using fourteen microsatellite loci. RESULTS: At population scale we showed strong genetic structure between the three sample sites. At the definitive host scale, we observed that host factors can shape the genetic composition of parasite infra-populations. First, in male patients, we observed a positive link between parasite genetic diversity and the age of the patients. Second, we observed a difference in genetic diversity which was high in human males, medium in human females and low in non-human primates (NHPs). Finally, whatever the transmission site no genetic structure was observed between human and non-human primates, however, there appears to be little barriers, if any, host specificity of the S. mansoni populations with cross-host infections. CONCLUSION: Occurrence of infection of a single host with multiple S. mansoni strains and inter- and intra-host genetic variations was observed. Substantial genetic diversity and gene flow across the S. mansoni population occurred at each site and non-human primates likely play a role in local transmission and maintenance of infection. Therefore, public health and wildlife professionals should work together to improve disease control and elimination strategies.

Painted black: Iguana melanoderma (Reptilia, Squamata, Iguanidae) a new melanistic endemic species from Saba and Montserrat islands (Lesser Antilles).

The Lesser Antilles, in the Eastern Caribbean, is inhabited by three Iguana species: the Lesser Antillean iguanaIguana delicatissima, which is endemic to the northernmost islands of the Lesser Antilles, the introduced common iguana from South America, Iguana iguana iguana, represented also by the two newly described endemic subspecies Iguana iguana sanctaluciae from Saint Lucia and Iguana iguana insularis from Saint Vincent and the Grenadines, and Grenada, and the introduced Iguana rhinolopha from Central America. Drawing on both morphological and genetic data, this paper describes the Iguana populations from Saba and Montserrat as a new species, Iguana melanoderma. This species is recognized on the basis of the following combination of characteristics: private microsatellite alleles, unique mitochondrial ND4 haplotypes, a distinctive black spot between the eye and tympanum, a dorsal carpet pattern on juveniles and young adults, a darkening of body coloration with aging (except for the anterior part of the snout), a black dewlap, pink on the jowl, the high number of large tubercular nape scales, fewer than ten medium sized-triangular dewlap spikes, high dorsal spikes, and lack of horns on the snout. This new melanistic taxon is threatened by unsustainable harvesting (including for the pet trade) and both competition and hybridization from escaped or released invasive alien iguanas (I. iguana iguana and I. rhinolopha) from South and Central America, respectively. The authors call for action to conserve Iguana melanoderma in Saba and Montserrat and for further research to investigate its relationship to other melanistic iguanas from the Virgin Islands and coastal islands of Venezuela.

A story of nasal horns: two new subspecies of Iguana Laurenti, 1768 (Squamata, Iguanidae) in Saint Lucia, St Vincent amp; the Grenadines, and Grenada (southern Lesser Antilles).

The Lesser Antilles, in the Eastern Caribbean, were long considered to have only two species in the genus Iguana Laurenti 1768: the Lesser Antillean iguana Iguana delicatissima, which is endemic to parts of the Lesser Antilles, and the Common green iguana Iguana iguana, which also occurs throughout Central and South America. No subspecies are currently recognised. However, herpetologists and reptile collectors have pointed out strong physical differences between some of the island populations of Iguana iguana and those from the continent. Drawing on both morphological and genetic data, this paper describes two subspecies of the Common green iguana Iguana iguana from the southern Lesser Antilles, specifically the countries of Saint Lucia Iguana iguana sanctaluciae and Iguana iguana insularis from St Vincent the Grenadines, and Grenada. The form on the island of Saint Vincent has not been identified. The new subspecies are described based on the following unique combination of characters: Presence of high median and medium to small lateral horns on the snout; Small subtympanic plate not exceeding 20% of the eardrum size; Two or three scales of decreasing size anterior to the subtympanic plate; Fewer than ten small to medium triangular gular spikes; Medium sized dewlap; Low number of small to medium dispersed nuchal tubercles; Dark brown iris, with the white of the eye visible; Oval, prominent nostril; Short and relatively flat head; High dorsal spines; No swelling of the jowls in reproductively active males.                Iguana iguana sanctaluciae has in adults vertical black stripes on body and tail and a black dewlap whereas Iguana iguana insularis is pale grey or creamy white in adults.                Both subspecies are globally threatened by unsustainable hunting (including the pet trade) and by invasive alien species,     including hybridization from invasive iguanas from South and Central America (I. iguana iguana and I. rhinolopha, considered here as full species) that have become established in all three countries. The authors call for stronger measures to conserve the remaining purebred Iguana i. insularis and Iguana i. sanctaluciae ssp. nov. throughout their ranges and for further research to identify other cryptic species and subspecies of Iguana in the Lesser Antilles.

When GIS zooms in: spatio-genetic maps of multipaternity in Armadillidium vulgare.

Geographic information system (GIS) tools are designed to illustrate, analyse and integrate geographic or spatial data, usually on a macroscopic scale. By contrast, genetic tools focus on a microscopic scale. Because in reality, landscapes have no predefined scale, our original study aims to develop a new approach, combining both cartographic and genetic approaches to explore microscopic landscapes. For this, we focused on Armadillidium vulgare, a terrestrial isopod model in which evolutionary pressures imposed by terrestrial life have led to the development of internal fertilisation and, consequently, to associated physiological changes. Among these, the emergence of internal receptacles, found in many taxa ranging from mammals to arthropods, allowed females to store sperm from several partners, enabling multipaternity. Among arthropods, terrestrial isopods like the polygynandrous A. vulgare present a female structure, the marsupium, in which fertilised eggs migrate and develop into mancae (larval stage). To test our innovative combined approach, we proposed different males to four independent females, and at the end of incubation in the marsupium, we mapped (using GIS methods) and genotyped (using 12 microsatellite markers) all the incubated mancae. This methodology permitted to obtain spatio-genetic maps describing heterozygosity and spatial distribution of mancae and of multipaternity within the marsupial landscape. We discussed the interest of this kind of multidisciplinary approach which could improve in this case our understanding of sexual selection mechanisms in this terrestrial crustacean. Beyond the interesting model-focused insights, the main challenge of this study was the transfer of GIS techniques to a microscopic scale and our results appear so as pioneers rendering GIS tools available for studies involving imagery whatever their study scale.

An American termite in Paris: temporal colony dynamics.

Termites of the genus Reticulitermes are widespread invaders, particularly in urban habitats. Their cryptic and subterranean lifestyle makes them difficult to detect, and we know little about their colony dynamics over time. In this study we examined the persistence of Reticulitermes flavipes (Kollar) colonies in the city of Paris over a period of 15 years. The aim was (1) to define the boundaries of colonies sampled within the same four areas over two sampling periods, (2) to determine whether the colonies identified during the first sampling period persisted to the second sampling period, and (3) to compare the results obtained when colonies were delineated using a standard population genetic approach versus a Bayesian clustering method that combined both spatial and genetic information. Herein, colony delineations were inferred from genetic differences at nine microsatellite loci and one mitochondrial locus. Four of the 18 identified colonies did not show significant differences in their genotype distributions between the two sampling periods. While allelic richness was low, making it hard to reliably distinguish colony family type, most colonies appeared to retain the same breeding structure over time. These large and expansive colonies showed an important ability to fuse (39% were mixed-family colonies), contained hundreds of reproductives and displayed evidence of isolation-by-distance, suggesting budding dispersal. These traits, which favor colony persistence over time, present a challenge for pest control efforts, which apply treatment locally. The other colonies showed significant differences, but we cannot exclude the possibility that their genotype distributions simply changed over time.

Isolation, characterization and PCR multiplexing of microsatellite loci for two sub-species of terrestrial isopod Porcellio dilatatus (Crustacea, Oniscidea).

Several microsatellite markers have already been developed for different terrestrial isopod species such as Armadillidium vulgare, A. nasatum and Porcellionides pruinosus. In all these species, the endosymbiont Wolbachia has a feminizing effect that generates a female bias in sex ratio and reduces the number of reproductive males. Thus this can potentially decrease the genetic diversity of host populations. However, in some other isopod species, Wolbachia induces cytoplasmic incompatibility (CI); the most commonly described effect of Wolbachia in arthropods. The CI by rendering some crossings incompatible can reduce the gene flow and strengthen genetic differentiation between isopod populations. To date, the influence of Wolbachia inducing CI on population structure of terrestrial isopods has never been investigated. In this study, we developed 10 polymorphic microsatellite markers shared by two sub-species of Porcellio dilatatus. Crossings between the two sub-species are partially incompatible due to two CI-inducing Wolbachia strains. These new microsatellite markers will allow us to investigate the effect of CI on host genetic differentiation in this species complex.

Multi-infections of feminizing Wolbachia strains in natural populations of the terrestrial isopod Armadillidium vulgare.

Maternally inherited Wolbachia (α-Proteobacteria) are widespread parasitic reproductive manipulators. A growing number of studies have described the presence of different Wolbachia strains within a same host. To date, no naturally occurring multiple infections have been recorded in terrestrial isopods. This is true for Armadillidium vulgare which is known to harbor non simultaneously three Wolbachia strains. Traditionally, such Wolbachia are detected by PCR amplification of the wsp gene and strains are characterized by sequencing. The presence of nucleotide deletions or insertions within the wsp gene, among these three different strains, provides the opportunity to test a novel genotyping method. Herein, we designed a new primer pair able to amplify products whose lengths are specific to each Wolbachia strain so as to detect the presence of multi-infections in A. vulgare. Experimental injections of Wolbachia strains in Wolbachia-free females were used to validate the methodology. We re-investigated, using this novel method, the infection status of 40 females sampled in 2003 and previously described as mono-infected based on the classical sequencing method. Among these females, 29 were identified as bi-infected. It is the first time that naturally occurring multiple infections of Wolbachia are detected within an individual A. vulgare host. Additionally, we resampled 6 of these populations in 2010 to check the infection status of females.

Isolation and characterization of microsatellite loci for the isopod crustacean Armadillidium vulgare and transferability in terrestrial isopods.

Armadillidium vulgare is a terrestrial isopod (Crustacea, Oniscidea) which harbors Wolbachia bacterial endosymbionts. A. vulgare is the major model for the study of Wolbachia-mediated feminization of genetic males in crustaceans. As a consequence of their impact on host sex determination mechanisms, Wolbachia endosymbionts are thought to significantly influence A. vulgare evolution on various grounds, including population genetic structure, diversity and reproduction strategies. To provide molecular tools for examining these questions, we isolated microsatellite loci through 454 pyrosequencing of a repeat-enriched A. vulgare genomic library. We selected 14 markers and developed three polymorphic microsatellite multiplex kits. We tested the kits on two A. vulgare natural populations and found high genetic variation, thereby making it possible to investigate the impact of Wolbachia endosymbionts on A. vulgare nuclear variation at unprecedented resolution. In addition, we tested the transferability of these kits by cross-species amplification in five other terrestrial isopod species harboring Wolbachia endosymbionts. The microsatellite loci showed good transferability in particular in Armadillidium nasatum and Chaetophiloscia elongata, for which these markers represent promising tools for future genetic studies.

Follow-up of the genetic diversity and snail infectivity of a Schistosoma mansoni strain from field to laboratory.

Schistosoma mansoni is an endoparasite causing a serious human disease called schistosomiasis. The quantification of parasite genetic diversity is an essential component to understand schistosomiasis epidemiology and disease transmission patterns but some studies on parasite genetic diversity are performed using parasite laboratory strains. However, a potential discrepancy in level of genetic variation between field populations and laboratory strains may have various implications in our deductions. In this study, 246 adult worms were analysed on 15 microsatellite markers to investigate variation of genetic diversity between a founder field isolate and the nine successive laboratory generations during three years of laboratory maintenance. In parallel, we measured a parasite life trait (snail infectivity) at each generation in order to test a potential link between inbreeding and snail infectivity. Our genetic analyses demonstrate a significant genetic differentiation between all parasite generations and a significant isolation by time associated with a decrease in neutral genetic diversity that is likely to be the result of successive bottleneck events. However, while snail infectivity decreases sharply between field isolate and the first laboratory generation, this parasite life trait does not evolve between other laboratory generations and appeared disconnected from this continuous neutral genetic diversity loss. We hypothesize that a sufficient level of compatibility polymorphism at a genomic level is maintained independently of an increase of inbreeding, ensuring the stability in the parasite life trait.