Origin and evolution of the bread wheat D genome.

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks1,2. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch's goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschii genomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.

Shared haemogregarine infections in competing lacertids.

In parasite­host interactions host species may differ in their ability to fight parasitic infections, while other ecological interactions, including competition, may differentially alter their physiological state, making them even more susceptible to parasites. In this study, we analyse the haemogregarine blood parasites infecting two competing lizard species, Iberolacerta horvathi and Podarcis muralis, and explore host­parasite relationships under different host competition scenarios. Both species were infected with haemogregarine parasites belonging to the genus Karyolysus. Using the 18S rRNA gene, six new Karyolysus haplotypes were identified clustering with other Central and Eastern European samples, and widely shared between both lizard hosts. Haemogregarine infections were detected at all sampled sites with over 50% of individuals parasitized. Overall, I. horvathi was more frequently and also more intensely parasitized than P. muralis, with higher infection rates observed in syntopy. Males of both species tended to be more frequently infected and showed a higher infection intensity than conspecific females. The results suggest that parasitisation by haemogregarines may be relevant in the dynamics of the competitive relationship between these lizard species. More studies, including immunological response analysis, and the identification of the vectors are needed to better understand host­parasite relationships and competition.

Blood parasite diversity (Apicomplexa: Haemogregarinidae) within the western populations of the European pond turtle Emys orbicularis.

Molecular tools have revolutionized assessments of blood parasites in freshwater turtles. In the Iberian Peninsula and North Africa, two native species of terrapins occur, Emys orbicularis (Linnaeus) and Mauremys leprosa (Schweigger). Both have been identified as hosts for the blood parasite Haemogregarina stepanowi Danilewsky, 1885, which has also been found in related species. However, recent assessments of M. leprosa have identified several distinct genetic lineages of these parasites in this host, while only three haemogregarine lineages were identified in E. orbicularis in Tunisia. Here, we screened 215 individuals of E. orbicularis from the Iberian Peninsula, Menorca Island and Morocco for haemogregarine parasites using partial 18S rRNA gene sequences to estimate relationships. Three unrelated lineages of parasites were detected, one presumed H. stepanowi and two lineages previously known from M. leprosa. A considerable undescribed diversity of parasites exists within these vertebrate host species, while mixed infection and host-sharing is also widespread. Considering that E. orbicularis is near threatened in this region, it is of great importance to identify the parasites infecting it, and to further assess the potential deleterious impact of these diverse parasites on their hosts.

Molecular phylogenetics of sub-Saharan African natricine snakes, and the biogeographic origins of the Seychelles endemic Lycognathophis seychellensis.

Phylogenetic relationships of sub-Saharan African natricine snakes are understudied and poorly understood, which in turn has precluded analyses of the historical biogeography of the Seychelles endemic Lycognathophis seychellensis. We inferred the phylogenetic relationships of Seychelles and mainland sub-Saharan natricines by analysing a multilocus DNA sequence dataset for three mitochondrial (mt) and four nuclear (nu) genes. The mainland sub-Saharan natricines and L. seychellensis comprise a well-supported clade. Two maximally supported sets of relationships within this clade are (Limnophis,Natriciteres) and (Afronatrix,(Hydraethiops,Helophis)). The relationships of L. seychellensis with respect to these two lineages are not clearly resolved by analysing concatenated mt and nu data. Analysed separately, nu data best support a sister relationship of L. seychellensis with (Afronatrix,(Hydraethiops,Helophis)) and mt data best support a sister relationship with all mainland sub-Saharan natricines. Methods designed to cope with incomplete lineage sorting strongly favour the former hypothesis. Genetic variation among up to 33 L. seychellensis from five Seychelles islands is low. Fossil calibrated divergence time estimates support an overseas dispersal of the L. seychellensis lineage to the Seychelles from mainland Africa ca. 43-25 million years before present (Ma), rather than this taxon being a Gondwanan relic.

Parasites in a hotspot: diversity and specificity patterns of apicomplexans infecting reptiles from the Socotra Archipelago.

Although parasites represent a major component of biodiversity, they remain poorly assessed, especially in remote regions. In this study, we screened 461 reptiles from Socotra, the largest and most biologically diverse archipelago in Arabia. Using 18S rRNA primers, we detected various apicomplexan parasites, namely haemogregarines, sarcocystids and eimeriids. Haemogregarines were the most common and genetically diverse, followed by sarcocystids (genus Sarcocystis) and eimeriids (genera Isospora and Lankesterella). All were related to parasites of other reptiles, including species from Arabia, Northern Africa and Asia. Like their 29 endemic reptile hosts, almost all Socotran parasites presented high genetic divergence and ecological differences from those found elsewhere, and probably represent undescribed endemic species. Among hosts, skinks were the most parasitized, which contrasted with similar studies from other areas, probably due to their more generalist diet and habitat use. As expected due to its high species richness, geckos harboured the highest parasite diversity in the archipelago. Parasite diversity also seemed to be correlated to island size, as the largest island harboured most haplotypes. This study emphasizes the importance of screening parasites in wild hosts from remote regions and of considering host ecology to understand disease transmission across taxa.

Invasive lizard has fewer parasites than native congener.

Invasive species can carry parasites to introduced locations, which may be key to understand the success or failure of species establishment and the invasive potential of introduced species. We compared the prevalence and infection levels of haemogregarine blood parasites between two sympatric congeneric species in Lisbon, Portugal: the invasive Italian wall lizard (Podarcis siculus) and the native green Iberian wall lizard (Podarcis virescens). The two species had significant differences in their infection levels: while P. virescens had high prevalence of infection (69.0%), only one individual of P. siculus was infected (3.7%), and while P. virescens exhibited an average intensity of 1.36%, the infected P. siculus individual had an infection rate of only 0.04%. Genetic analyses of 18S rRNA identified two different haemogregarine haplotypes in P. virescens. Due to the low levels of infection, we were not able to amplify parasite DNA from the infected P. siculus individual, although it was morphologically similar to those found in P. virescens. Since other studies also reported low levels of parasites in P. siculus, we hypothesize that this general lack of parasites could be one of the factors contributing to its competitive advantage over native lizard species and introduction success.

Characterization and identification of haemogregarine hemoparasites (Apicomplexa: Adeleina: Hepatozoidae) in natural populations of Mauremys leprosa leprosa and M. leprosa saharica from Morocco.

Distribution, prevalence and parasitaemia of apicomplexan parasites of the genus Haemogregarina were studied in 858 freshwater turtles (735 Mauremys leprosa leprosa and 123 Mauremys leprosa saharica) throughout 30 localities from Morocco. Blood smears were collected from the turtles and partial 18S rRNA sequence data used to infer genetic diversity and phylogenetic relationships. Of the 858 individuals analyzed by microscopy 22.7% were infected, from 16 M. leprosa leprosa localities. Individuals of M. leprosa saharica sampled south of the High Atlas Mountains were not infected, probably due to the absence or rarity of the leech vectors in these localities. Within M. leprosa leprosa, we did not identify any patterns between geography and prevalence, which varied between 10% (Oued Nfiss) to 100% (Oued Tassaout). Five distinct genetic lineages were identified, indicating the likely presence of multiple species of haemogregarines, one of which probably corresponds to Haemogregarina stepanowi. Mixed infections were also detected. Additional studies are needed to better understand the ecology and epidemiology of this parasite in turtles, as well as the host-parasite relationship with their definitive hosts, leeches.

Absence of Hemolivia mauritanica (Apicomplexa: Haemogregarinidae) in natural populations of Testudo graeca in Morocco.

During spring 2018, we captured 101 spur-thighed tortoises, Testudo graeca, from seven localities in central Morocco. All tortoises were examined for the presence of blood parasites Hemolivia mauritanica and Hyalomma aegyptium ticks, the known vectors. We looked for H. mauritanica infection by examination of blood smears and by genetic analysis with PCR using extractions from both tortoises and ticks. On all tortoises collected, 71.29% were infested with at least one tick, with a mean infestation intensity of 7.12 ticks/tortoise and maximum of 15.55 ticks/tortoises in Had Draa locality (Essaouira region). Although the definitive host is present and abundant in all tortoise populations, all blood samples were Hemolivia-negative. Our results support and confirm the finding of studies previously conducted in other populations of Morocco and indicate that H. mauritanica has a narrower distribution range than its tick vector.

A paradise for parasites? Seven new haemogregarine species infecting lizards from the Canary Islands.

Oceanic islands are hotspots of biodiversity due to their high levels of endemism, with the Canary Islands being a notable example. A previous molecular study on the biogeography and host associations of haemogregarines (Apicomplexa: Adeleorina) infecting lizards from this archipelago detected seven parasite haplogroups. These haplogroups exhibited high host-specificity and geographical structure, suggesting that they might correspond to distinct biological identities. In this study, along with sequencing a longer fragment of the 18S rRNA, we further explore the distinctiveness of these parasites by analysing their morphology, effects on host erythrocytes and parasitaemia levels. These lines of evidence together with their genetics, host associations, frequency of occurrence and geographical distribution support them as different biological entities. As such, we describe seven new species: Karyolysus canariensis sp. nov., Karyolysus galloti sp. nov., Karyolysus stehlini sp. nov., Karyolysus gomerensis sp. nov., Karyolysus atlanticus sp. nov., Karyolysus tinerfensis sp. nov. and Karyolysus makariogeckonis sp. nov. These new taxa are further examples of endemic diversity in the Canarian archipelago. They also contribute to clarify the taxonomy within the Apicomplexa, a phylum estimated to have one of the lowest percentages of described species.

Getting there and around: Host range oscillations during colonization of the Canary Islands by the parasitic nematode Spauligodon.

Episodes of expansion and isolation in geographic range over space and time, during which parasites have the opportunity to expand their host range, are linked to the development of host-parasite mosaic assemblages and parasite diversification. In this study, we investigated whether island colonization events lead to host range oscillations in a taxon of host-specific parasitic nematodes of the genus Spauligodon in the Canary Islands. We further investigated whether range oscillations also resulted in shifts in host breadth (i.e., specialization), as expected for parasites on islands. Parasite phylogeny and divergence time estimates were inferred from molecular data with Bayesian methods. Host divergence times were set as calibration priors after a priori evaluation with a global-fit method of which individual host-parasite associations likely represent cospeciation links. Parasite colonization history was reconstructed, followed by an estimation of oscillation events and specificity level. The results indicate the presence of four Spauligodon clades in the Canary Islands, which originated from at least three different colonization events. We found evidence of host range oscillations to truly novel hosts, which in one case led to higher diversification. Contemporary host-parasite associations show strong host specificity, suggesting that changes in host breadth were limited to the shift period. Lineages with more frequent and wider taxonomic host range oscillations prior to the initial colonization event showed wider range oscillations during colonization and diversification within the archipelago. Our results suggest that a lineage's evolutionary past may be the best indicator of a parasite's potential for future range expansions.

Underground cryptic speciation within the Maghreb: Multilocus phylogeography sheds light on the diversification of the checkerboard worm lizard Trogonophis wiegmanni.

Biogeographic and evolutionary patterns in the North African portion of the Western Palaearctic are poorly known. A high fraction of undescribed diversity is expected in this region, especially in groups such as reptiles. Here we used mitochondrial (12S, 16S, cytb) and nuclear (pomc, rag2, cmos) markers and morphological data to investigate phyletic diversification and phylogeographical structure in the amphisbaenian Trogonophis wiegmanni endemic to the Maghreb. Phylogenetic and molecular dating analyses based on gene trees and species trees support three deeply divergent lineages of Pliocene origin, two in Morocco and one in central Algeria and Tunisia. Parapatry, reciprocal monophyly, high genetic divergence and limited morphological differentiation between them suggest that these lineages represent independent cryptic taxonomic units. Emerging lines of evidence from this study and from available literature on Maghreb taxa support (i) a major biogeographic break between western and eastern Maghreb and (ii) a role of the Atlas as a biogeographic divide within the western Maghreb (Morocco). The origin of these biogeographic units is probably associated with the evolutionary events prompted by the Late Miocene palaeogeographic setting and later by Plio-Pleistocene climatic changes and their interplay with prominent orographic barriers within North Africa.

The taxonomy of the Tarentola mauritanica species complex (Gekkota: Phyllodactylidae): Bayesian species delimitation supports six candidate species.

The lack of morphological diagnosable characters typical of cryptic species, poses a particular problem to taxonomists. This is especially true when taxa are closely related, sharing considerable amounts of ancestral polymorphism. Phylogenetic studies on the Moorish gecko species-complex, Tarentola mauritanica, uncovered extremely high levels of mtDNA diversity with six identified clades, including one from the Canary Islands identified as T. angustimentalis. Because of the conserved morphology of this species and its paraphyletic status with respect to T. angustimentalis, it was suggested that T. mauritanica is a cryptic species complex. Nevertheless, none of the nuclear loci used were reciprocally monophyletic regarding the mitochondrial lineages due to retention of ancestral polymorphism. In this study, we added three new intron markers to the already available dataset and used additional tools, namely phylogenetic gene trees, species tree and species limits within a Bayesian coalescent framework to confirm the support of the main lineages. Bayesian clustering analysis supports all six mtDNA lineages as independent groups, despite showing signs of ancestral polymorphism or possibly gene flow between the Maghreb/South Iberia and Central Morocco clades. The species tree recovered two major groups; one clustering taxa from Europe and Northern Maghreb and another one encompassing the lineages from Central/Southern Morocco, Central Morocco and Canary Islands, indicating that the ancestor of T. angustimentalis came from the Central/Southern Morocco region. Finally, Bayesian coalescent species delimitation analysis supports all six mitochondrial clades as "unconfirmed candidate species", pending morphological data to define them.

Patterns of genetic diversity in Hepatozoon spp. infecting snakes from North Africa and the Mediterranean Basin.

Species of Hepatozoon Miller, 1908 are blood parasites most commonly found in snakes but some have been described from all tetrapod groups and a wide variety of hematophagous invertebrates. Previous studies have suggested possible associations between Hepatozoon spp. found in predators and prey. Particularly, some saurophagous snakes from North Africa and the Mediterranean region have been found to be infected with Hepatozoon spp. similar to those of various sympatric lizard hosts. In this study, we have screened tissue samples of 111 North African and Mediterranean snakes, using specific primers for the 18S rRNA gene. In the phylogenetic analysis, the newly-generated Hepatozoon spp. sequences grouped separately into five main clusters. Three of these clusters were composed by Hepatozoon spp. also found in snakes and other reptiles from the Mediterranean Basin and North Africa. In the other two clusters, the new sequences were not closely related to geographically proximate known sequences. The phylogeny of Hepatozoon spp. inferred here was not associated with intermediate host taxonomy or geographical distribution. From the other factors that could explain these evolutionary patterns, the most likely seems series of intermediate hosts providing similar ribotypes of Hepatozoon and a high prevalence of host shifts for Hepatozoon spp. This is indicated by ribotypes of high similarity found in different reptile families, as well as by divergent ribotypes found in the same host species. This potentially low host specificity has profound implications for the systematics of Hepatozoon spp.

What you get is what they have? Detectability of intestinal parasites in reptiles using faeces.

Parasitological analyses are often based on invasive methodologies, involving host sacrifice, raising ethical and conservation issues. However, alternative non-invasive approaches may not be always applicable due to the location of the parasite in the host tissue or the quality and reliability of the non-invasive sample per se. In this study, we compare the differences in detectability of intestinal parasites in reptiles using the classical invasive approach (intestine dissection), versus a non-invasive procedure (faecal examination), collected from the same individual host. Our results showed significantly lower detectability of helminths in faeces versus the intestine. Moreover, the number of parasites found in faeces was not explained either by the intensities found in the respective intestine or by the host identity. Several factors may explain the lack of association between the two types of samples, but more importantly, our results highlight the randomness of the presence of parasites in faeces. Even if it is not recommended that comparative studies of either parasite abundance or parasite communities be conducted on the basis of faecal samples, there are other types of studies (i.e. genetic) that can be performed with this source of information, thus avoiding the sacrifice of the host. Due to their wide spectrum of life stages and localization in the host tissue, parasites are challenging candidates for non-invasive sampling and consequently, parasitological methodologies should be carefully selected according to the objective of the study.

What Influences the Prevalence and Intensity of Haemoparasites and Ectoparasites in an Insular Lizard?

Island biogeography theories predict that characteristics such as island size, age, and isolation interplay in host-parasite dynamics. In this study, we analyzed haemogregarines of the Aegean wall lizard, Podarcis erhardii, to investigate how island characteristics relate to parasite prevalence and intensity. A previous assessment of 19 Greek island populations suggested that isolation time and host population density were key predictors of haemogregarines. Here, by combining microscopy and genetic techniques, we extend this previous study to four additional islands: Syros, Folegandros, Santorini and Nea Kameni. We also recorded the prevalence of ticks and mites, definitive hosts for these parasites. The genetically identified haemogregarines are part of a clade with parasites from other lizard species, including some considered as Karyolysus, but others assigned to Hepatozoon. The prevalence of these parasites differed significantly between islands, while their intensity did not. The presence of ticks was associated with endoparasite prevalence, and males were more frequently infected by haemogregarines than females. Combining our data with that of the previous study, we found no significant impact of the island age and area on parasite prevalence. We also confirmed the presence of the unrelated parasite genus Schellackia through microscopy and DNA sequencing, which is the first record of this genus in this host species. Our results further highlight the complexity of host-parasite systems.

Molecular survey and microscopic examination of Hepatozoon Miller, 1908 (Apicomplexa: Adeleorina) in lacertid lizards from the western Mediterranean.

The genus Hepatozoon Miller, 1908 (Apicomplexa: Adeleorina) is composed of intracellular haemogregarine parasites that are widely distributed among all tetrapod groups. The present study combines microscopic and molecular data on haemogregarine parasites from lizards in the western Mediterranean. We screened tissue samples and examined blood smears for the presence of species of Hepatozoon from four lizards, namely Algyroides marchi Valverde, endemic to Southeast Spain, Podarcis bocagei Seoane from Spain and Portugal, P hispanica Steindachner from Spain, and P lilfordi Günther from Cabrera, Balearic Islands (Spain). Our results show that prevalence and intensity of Hepatozoon parasites vary between and within lizard species from different regions. Algyroides marchi and P bocagei from Spain had the lowest values, whereas P hispanica had the highest. Phylogeny based on 18S rRNA gene sequences indicates that most of the new Hepatozoon sequences are part of a clade exclusive from North African and Iberian lizards, except for a single P bocagei isolate that is found related to another clade including isolates from other reptile host species and rodents. Interestingly, isolates from Algyroides form a distinct monophyletic subgroup, which could be a signal of strict host-specificity within this host genus.

Discordant phylogeographic patterns between the tortoise tick Hyalomma aegyptium and their Testudo graeca hosts.

Tortoise ticks, Hyalomma aegyptium, are considered so strongly associated with their hosts that they are even used as indirect indicators for them. In such a case, a robust pattern of congruence between host and parasite could be expected, with phylogeographic breaks within the host being reflected in their parasites. We sequenced two mitochondrial partial gene regions (12S rRNA and Cytochrome Oxidase 1) from ticks across northern Africa and Anatolia, and compared patterns of variation with those identified in its main host, Testudo graeca. Two distinct haplogroups were identified, both of which were found distributed across much of northern Africa. This pattern does not reflect the known variation within the host, which has multiple, geographically disjunct subspecies in this region, but rather the major climatic zones. This relationship can be explained by adaptive processes to environmental conditions influenced by the climate, as well as by the spatial structure of the communities of tick potential hosts in larval and nymphal stages. Extensive anthropogenic movement of tortoises may also obscure congruence patterns between H. aegyptium ticks and their hosts.

The unexpected gecko: A new cryptic species within Urocotyledon inexpectata (Stejneger, 1893) from the northern granitic Seychelles.

Urocotyledon inexpectata, a small gecko endemic to the granitic islands of the Seychelles, has previously been demonstrated to comprise two highly distinct clades based on mitochondrial and nuclear DNA sequences, with one lineage exclusive to a northern group of islands, and the second lineage exclusive to the more southerly islands. Here we complement the genetic data with additional analyses to determine if the clades should be considered distinct species. We present and analyse new morphological data, including skull and jaw osteology, and supplement the available genetic data with DNA sequences for individuals from the previously unsampled island of Felicit, which cluster with the other northern island samples. Despite the high morphological similarity between Urocotyledon populations from northern and southern islands, diagnostic characters were identified, with the northern lineage having a more completely ossified skull, more tooth loci on maxilla and dentary, shorter hindlimbs, relatively smaller eye diameter and relatively wider head. We therefore describe the northern lineage as a distinct species, Urocotyledon norzilensis sp. nov., and discuss the biological and conservation management implications of this taxonomic action.

Digging in a 120 years-old lunch: What can we learn from collection specimens of extinct species?

Studying collection specimens is often the only way to unravel information about recent extinctions. These can reveal knowledge on threats and life traits related to extinction, and contribute, by extrapolation, to the conservation of extant species. However, high-throughput sequencing methods have rarely been applied to extinct species to reveal information on their ecology. Insular species are especially prone to extinction. We studied the gut contents of three specimens of the extinct giant skink Chioninia coctei of the Cabo Verde Islands using microscopy and DNA-metabarcoding. The presence of Tachygonetria adult nematodes suggests plants as important diet items. Our metabarcoding approach also identified plants and, additionally, invertebrates, supporting the hypothesis of C. coctei's generalist diet. The absence of vertebrates in the digestive contents may reflect the decline of seabirds on the Desertas Islands that could have contributed to the debilitation of the giant skink, already depleted by persecution and severe droughts. Even with a small sample size, this study contributes to shedding light on the trophic roles of this enigmatic extinct species and emphasizes the need to develop holistic conservation plans for island threatened taxa. Additionally, it illustrates the potential of integrating up-to-date molecular methods with traditional approaches to studying collection specimens to help to solve ecological puzzles in other ecosystems.

Diversity of microorganisms in Hyalomma aegyptium collected from spur-thighed tortoise (Testudo graeca) in North Africa and Anatolia.

Ticks carry a diverse community of microorganisms including non-pathogenic symbionts, commensals, and pathogens, such as viruses, bacteria, protozoans, and fungi. The assessment of tick-borne microorganisms (TBM) in tortoises and their ticks is essential to understand their eco-epidemiology, and to map and monitor potential pathogens to humans and other animals. The aim of this study was to characterize the diversity of microorganisms found in ticks collected from the spur-thighed tortoise (Testudo graeca) in North Africa and Anatolia. Ticks feeding on wild T. graeca were collected, and pathogens were screened by polymerase chain reaction using group-specific primers. In total, 131 adult Hyalomma aegyptium ticks were collected from 92 T. graeca in Morocco (n = 48), Tunisia (n = 2), Algeria (n = 70), and Turkey (n = 11). Bacteria and protozoa detected included Hemolivia mauritanica (22.9%), Midichloria mitochondrii (11.4%), relapsing-fever borreliae (8.4%), Ehrlichia spp. (7.6%), Rickettsia spp. (3.4%), Borrelia burgdorferi s.l. (0.9%), Francisella spp. (0.9%), and Wolbachia spp. (0.8%). The characterization of Rickettsia included R. sibirica mongolitimonae (Algeria), R. aeschlimannii (Turkey), and R.africae (Morocco). Hemolivia mauritanica and Ehrlichia spp. prevalence varied significantly with the sampling region/country. We did not detect significant associations in microorganism presence within ticks, nor between microorganism presence and tick mitochondrial DNA haplogroups. This is the first report of Francisella persica-like, relapsing fever borreliae, M. mitochondrii, and Wolbachia spp. in H. aegyptium ticks collected from wild hosts from the South and Eastern Mediterranean region, and of R. sibirica mongolitimonae and R. africae in H. aegyptium from Algeria and Morocco, respectively. Given that T. graeca is a common species in commercial and non-commercial pet trade, the evaluation of the role of this species and its ticks as hosts for TBM is particularly relevant for public health.