Molecular (ISSR, cp DNA, ITS) and Morphological Study of the Genus Tragopogon L. (Asteraceae)

Tragopogon L. (Cichorioideae, Lactuceae, Scorzonerinae) is an Old World genus with 150 species, Rechinger in Flora Iranica divided this genus in 13 section and 37 species that 26 species of them are exist in Iran. Safavi et al. divided it into 26 species without sections in flora Iran. Despite the anatomical and molecular studies done around the world, the exact classification of this genus is not clear due to the high number of secret species, hybridization, polyploidy and rapid diversification. The morphology studies of 32 species and Molecular studies (ISSR, ITS, cp DNA) of 22 species of the genus Tragopogon was investigated . The purpose of these studies are classification and determination of interspecific relationship in this genus. Sections of Rubriflori, Sosnowskya, Chromopappus, Majores, Angustissimi, Krascheninnikovia in flora of Iranica are confirmed on the basis of morphometry and molecular data. Section of Profundisulcati in flora Iranica is confirmed on the base of morphometry data. The Species of T. jesdianus, T . porphyrocephalus, T. rezaiyensis and T. Stroterocarpus in the flora of Iranica are not classified in any section which we classified in the Rubriflori section, Cp DNA dendrogram are not useful for classification in this genus and Chloroplast sequences are very similar among Tragopogon species, Therefore, the use of cp DNA markers in the classification of this genus is not recommended.

Identification of Wolf-Dog Hybrids in Europe – An Overview of Genetic Studies

Significant development of genetic tools during the last decades provided opportunities for more detailed analyses and deeper understanding of species hybridization. New genetic markers allowed for reliable identification of admixed individuals deriving from recent hybridization events (a few generations) and those originating from crossings up to 19 generations back. Implementation of microsatellites (STRs) together with Bayesian clustering provided abundant knowledge regarding presence of admixed individuals in numerous populations and helped understand the problematic nature of studying hybridization (i.a., defining a reliable thresholds for recognizing individuals as admixed or obtaining well-grounded results representing actual proportion of hybrids in a population). Nevertheless, their utilization is limited to recent crossbreeding events. Single Nucleotide Polymorphisms (SNPs) proved to be more sensible tools for admixture analyses furnishing more reliable knowledge, especially for older generation backcrosses. Small sets of Ancestry Informative Markers (AIMs) of both types of markers were effective enough to implement in monitoring programs, however, SNPs seem to be more appropriate because of their ability to identify admixed individuals up to 3rd generations. The main aim of this review is to summarize abundant knowledge regarding identification of wolf-dog hybrids in Europe and discuss the most relevant problems relating to the issue, together with advantages and disadvantages of implemented markers and approaches.

Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core

Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.

The interaction between Tu-Izumo1 and Tu-JUNO is involved in turtles hybridization

The specificity of sperm-egg recognition is crucial to species independence, and two proteins (Izumo1 and JUNO) are essential for gamete adhesion/fusion in mammals. However, hybridization, which is very common in turtles, also requires specific recognition of sperm-egg binding proteins. In this study, we discovered that natural selection plays an important role in the codon usage bias of Tu-Izumo1 and Tu-JUNO. Positively selected sites and co-evolutionary analyses between Tu-Izumo1 and Tu-JUNO has been previously reported, and we confirm these results in a larger analysis containing 25 turtle species. We also showed that Tu-JUNO is expressed on the oocyte surface and that Tu-Izumo1 and Tu-JUNO interact with each other directly in different species hybridization combinations. Co-immunization assays revealed that this interaction is evolutionarily conserved in turtles. The results of avidity-based extracellular interaction screening between Tu-Izumo1 and Tu-JUNO for sperm-oocyte binding pairs (both within and across species) likely suggest that the interaction force between Izumo1 and JUNO has a certain correlation in whether the turtles can hybridize. Our results lay a theoretical foundation for the subsequent development of techniques to detect whether different turtle species can interbreed, which would provide the molecular basis for breeding management and species protection of turtles.

Geographic parthenogenesis in the brown alga Scytosiphon lomentaria (Scytosiphonaceae): sexuals in warm waters and parthenogens in cold waters

Geographic parthenogenesis (GP), a phenomenon where parthenogens and their close sexual relatives inhabit distinct geographic areas, has been considered an interesting topic to understand the adaptation to marginal habitats and the role of hybridization in evolution. Reports of GP from land and freshwater are numerous, however, this occurrence has been rarely reported on from the sea. Brown algae are mostly marine and are thought to include numerous obligate parthenogens; still, little is known about the distribution, origin, and evolution of parthenogens in this group. Here we report a novel pattern of GP in the isogamous brown alga Scytosiphon lomentaria. Sex ratio investigation demonstrated that, in Japan, sexual populations grew in the coast along warm ocean currents, whereas female-dominant parthenogenetic populations grew mainly in the coast along a cold ocean current. In the two localities where sexual and parthenogenetic populations were parapatric, parthenogens grew in more wave-exposed areas than sexuals. Population genetic and phylogenetic analyses, including those based on genome-wide single nucleotide polymorphism data, suggested that: (1) parthenogens evolved at least twice in S. lomentaria, (2) parthenogens did not originate from inter-species hybridization, (3) new parthenogenetic lineages have arisen from hybridizations between parthenogens and sexuals, and (4) parthenogens have a wider distribution than sexuals. We also showed that the production of sex pheromones, which attract male gametes, has been independently suppressed/lost in two parthenogenetic lineages. This parallel suppression/loss of the sexual trait may represent the direct origin of parthenogens, or the regressive evolution of a useless trait under asexuality.

Diverging patterns of introgression from Schistosoma bovis across S. haematobium African lineages

Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma species that can cause important public health and veterinary issues. In particular hybrids between Schistosoma haematobium and S. bovis associated with humans and animals respectively are frequently identified in Africa. Recent genomic evidence indicates that some S. haematobium populations show signatures of genomic introgression from S. bovis. Here, we conducted a genomic comparative study and investigated the genomic relationships between S. haematobium, S. bovis and their hybrids using 19 isolates originating from a wide geographical range over Africa, including samples initially classified as S. haematobium (n = 11), S. bovis (n = 6) and S. haematobium x S. bovis hybrids (n = 2). Based on a whole genomic sequencing approach, we developed 56,181 SNPs that allowed a clear differentiation of S. bovis isolates from a genomic cluster including all S. haematobium isolates and a natural S. haematobium-bovis hybrid. All the isolates from the S. haematobium cluster except the isolate from Madagascar harbored signatures of genomic introgression from S. bovis. Isolates from Corsica, Mali and Egypt harbored the S. bovis-like Invadolysin gene, an introgressed tract that has been previously detected in some introgressed S. haematobium populations from Niger. Together our results highlight the fact that introgression from S. bovis is widespread across S. haematobium and that the observed introgression is unidirectional.

The gene pool of the black apricot - Prunus dasycarpa Pers. and its use in stone fruit crops breeding

The article presents the results of research aimed at studying varieties, forms and hybrids of black apricot – Prunus dasycarpa Pers., preserved in the gene pool of the Krymsk EBS, VIR Branch, and identifying the feasibility of including genotypes of this species and hybrid seedlings in breeding programs to create new adaptive varieties with high fruit quality and easy vegetative reproduction of clonal rootstocks of stone fruit crops. It was revealed that cross-species hybridization of black apricot with stone fruit crops, in particular apricot and cherry plum, allows to create adaptive genotypes suitable for cultivation, as well as being a valuable source material for further breeding use. For production use, the varieties of the Krymsk EBS breeding are of interest: black apricot - Kubansky Cherny (45234)*, Cherny Barkhat (45235)*, Kolibri (45240)*, Plemkot Kubansky (26217)*; Russian plum Globus (43854)*; clonal rootstock Alab 1 (18213)* (*VIR catalogue No.).

Microevolutionary relationships between biotypes of Elymus confusus, E. peschkovae, and E. sibiricus (Poaceae) according to hybridization and sequencing of the nuclear gene GBSS1 (waxy)

According to descriptions, the Siberian species E. peschkovae and E. confusus differ in the presence or absence of trichomes on lemma and rachilla surfaces only. Two methods were used for study microevolutionary relationships between these species: hybridization of biotypes from different locations and analysis of nucleotide sequences of the low-copy nuclear gene GBSS1. Created and grown hybrids in combinations AMU-8804 × BER-0807 and AMU-8804 × BUK-1109 showed complete seed sterility in two field vegetations. Taking into account wide species areas, 3 hybrids were created between Magadan biotypes from a common habitat in the combination E. confusus MOL1887 × E. peschkovae MOL-1882. The plants showed seed fertility (SF) of 0–3 %. This result does not obscure the possibility to assess SF in the F2 generation and the character of inheritance of diagnostic traits. A comparative study of the GBSS1 gene sequences in accessions was carried out in comparison with clones of reference species. Differentiation of clones by the St2 subgenome in E. confusus, E. peschkovae, E. sibiricus and E. caninus did not reveal a clear relationships between the species. Meanwhile, a certain species specificity for the H1 subgenome was noted, confirming the existence of microevolutionary isolation of these species.

Utility of a high-resolution mouse single nucleotide polymorphism microarray assessed for rodent comparative genomics

In the study of genetic diversity in non-model species there is a notable lack of the low-cost, high resolution tools that are readily available for model organisms. Genotyping microarray technology for model organisms is well-developed, affordable, and potentially adaptable for cross-species hybridization. The Mouse Diversity Genotyping Array (MDGA), a single nucleotide polymorphism (SNP) genotyping tool designed for Mus musculus, was tested as a tool to survey genomic diversity of wild species for inter-order, inter-genus, and intra-genus comparisons. Application of the MDGA cross-species provides genetic distance information that reflects known taxonomic relationships reported previously between non-model species, but there is an underestimation of genetic diversity for non-Mus samples, indicated by a plateau in loci genotyped beginning 10-15 millions of years divergence from the house mouse. The number and types of samples included in datasets genotyped together must be considered in cross-species hybridization studies. The number of loci with heterozygous genotypes mapped to published genome sequences indicates potential for cross-species MDGA utility. A case study of seven deer mice yielded 159,797 loci (32% of loci queried by the MDGA) that were genotyped in these rodents. For one species, Peromyscus maniculatus, 6,075 potential polymorphic loci were identified. Cross-species utility of the MDGA provides needed genetic information for non-model species that are lacking genomic resources. Genotyping arrays are widely available, developed tools that are capable of capturing large amounts of genetic information in a single application, and represent a unique opportunity to identify genomic variation in closely related species that currently have a paucity of genomic information available. A candidate list of MDGA loci that can be utilized in cross-species hybridization studies was identified and may prove to be informative for rodent species that are known as environmental sentinels. Future studies may evaluate the utility of candidate SNP loci in populations of non-model rodents.Author SummaryThere is a need for a tool that can assay DNA sequence differences in species for which there is little or no DNA information available. One method of analyzing differences in DNA sequences in species with well-understood genomes is through a genotyping microarray, which has demonstrated utility cross-species. The Mouse Diversity Genotyping Array (MDGA) is a tool designed to examine known differences across the genome of the house mouse, Mus musculus. Given that related organisms share genetic similarity, the MDGA was tested for utility in identifying genome variation in other wild mice and rodents. Variation identified from distantly related species that were not of the same genus as the house mouse was an underestimate of the true amount of variation present in the genomes of wild species. Utility of the MDGA for wild species is best suited to mice from the same genus as the house mouse, and candidate variation identified can be tested in rodent populations in future studies. Identifying changes in genetic variation within populations of wild rodents can help researchers understand the links between specific genome changes and the ability to adapt to pressures in the environment, as well as better understand the evolution of rodents.