Genetic Introgression Between Different Groups Reveals the Differential Process of Asian cultivated Rice

Genetic introgression plays an important role in the domestication of crops. The Asian cultivate rice consists of two major subspecies, they are indica and japonica. There are already many reports about existence of genetic introgression between the two subspecies. However, those studies often use few limited markers to characterize the genetic introgression that exists in some specific small populations. In this study we use the genome wide variation data of Asia cultivated rice to investigate their genetic introgression on the whole genome level. We detect a total of 13 significantly high introgression loci between the tropical japonica and indica population. Two different methods are used to identify the genetic introgression regions. For most of the detected introgression regions they generally get consistent results. Some previous known introgression genes are detected in the identified introgression loci, such as heat resistance gene TT1 and GLW7. The biological functions for these genetic introgression regions are annotated by the published QTL mapping results. We find that genetic introgression plays an important role in both the determination of the phenotype and the domestication process of different groups. Our study also provides useful information and resources for the study of rice gene function and domestication process.

Identification of Natural Hybrids between Ahlbergia frivaldszkyi (Lederer, 1853) and Callophrys rubi (Linnaeus, 1758) (Lepidoptera, Lycaenidae) Using Mitochondrial and Nuclear Markers

Natural hybridization is rather widespread and common in animals and can have important evolutionary consequences. In terms of taxonomy, exploring hybridization and introgression is crucial in defining species boundaries and testing taxonomic hypotheses. In the present paper, we report on natural hybrid specimens between Ahlbergia frivaldszkyi (Lederer, 1853) and Callophrys rubi (Linnaeus, 1758). To test the hypothesis of their hybrid origin, we employed the molecular mitochondrial (COI gene) and nuclear (wingless, RPS5, and Ca-ATPase genes) markers commonly used in phylogenetic studies and explored the morphology of the specimens. Our analysis revealed that hybrids bear mitochondrial haplotypes of C. rubi, while nuclear fragments are heterozygous, sharing a combination of A. frivaldszkyi and C. rubi lineages. The hybrid specimens combine morphological characters of both genera. Our results for the first time empirically demonstrate the possibility of genetic introgression between these species and between the genera Callophrys and Ahlbergia on the whole.

Genetic Diversity and Population Structure of Wild Beets (Beta spp.) from the Western Iberian Peninsula and the Azores and Madeira Islands

In this work, using simple sequence repeat (SSR) markers, we present new insights into the genetic diversity, differentiation, and structure of Beta vulgaris subsp. maritima of western Iberia and the Azores and Madeira islands and of B. macrocarpa from southern Portugal. B. macrocarpa occurs only in southern Portugal and frequently in sympatry with B. vulgaris subsp. maritima, showing genetic introgression. B. macrocarpa has a better-defined structure than B. vulgaris subsp. maritima, which has a high degree of admixture. A great differentiation (FST ranging from 0.277 to 0.184) was observed among the northern populations of B. vulgaris subsp. maritima. In contrast, only a small differentiation (FST ranging from 0.000 to 0.026) was detected among the southern B. vulgaris subsp. maritima populations. The inland B. vulgaris subsp. maritima populations (“RIO” and “VMT”) are distinct from each other, which also occurs with the two islands’ populations (“MAD” and “AZO”). The existence of two distinct Atlantic Sea currents can explain the fact that Madeira is related to the southern populations, while the Azores is related to the northern populations. We consider that understanding the relationships existing within Beta spp. is key to future genetic studies and for the establishment of conservation measures. Our results show that the southern coastal areas of Portugal should be considered as a potential site for in situ conservation of the beet wild relatives. Special attention is needed in what concerns B. macrocarpa because this is a rare species that also occurs in a sympatric relationship with B. vulgaris subsp. maritima.

Quaternary geomorphological and climatic changes associated with the diversification of Iberian freshwater fishes: the case of the genus Cobitis (Cypriniformes, Cobitidae)

We studied the population genetic structure of Cobitis vettonica, an endangered freshwater fish species endemic to the Iberian Peninsula in order to propose a biogeographic model of the responses of species to the multiple changes that occurred in the Iberian hydrological system during the Quaternary period. We also deciphered the relationship of C. vettonica with its sister species C. paludica, particularly in sympatric areas and provide genetic information for conservation purposes. To achieve this end, we analysed both mitochondrial and nuclear data (the cytochrome b and the nuclear recombination activating 1 genes) and a battery of single nucleotide polymorphisms (SNPs) of 248 individuals of C. vettonica or C. paludica from 38 localities, including some sympatric ones, covering the entire distribution area of C. vettonica. We highlight the important role played by the hydrogeomorphological processes and climatic changes that occurred in the Iberian Peninsula during the Quaternary on both the population structure of C. vettonica and its relationship with its sister species C. paludica. Our results support the genetic introgression of populations at the eastern limit of the distribution of C. vettonica. Furthermore, we postulate genetic introgression in sympatric areas. Finally, we propose the establishment or expansion of four OCUs for C. vettonica, and highlight the threat faced by its populations due to the low level of genetic diversity detected for some of its populations and genetic introgression with C. paludica, which could eventually displace C. vettonica, resulting in a loss of diversity in this species.

Means, motive, and opportunity for biological invasions: genetic introgression in a fungal pathogen

Invasions by fungal plant pathogens pose a significant threat to the health of agriculture ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses in crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen on soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2 to 30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "The Means, Motive, and Opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographic areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.

Mate choice enhances post-zygotic barriers to gene flow via ancestry bundling

Hybridization and subsequent genetic introgression are now known to be common features of the histories of many species, including our own. Following hybridization, post-zygotic selection tends to purge introgressed DNA genome-wide. While mate choice can prevent hybridization in the first place, it is also known to play an important role in post-zygotic selection against hybrids, and thus the purging of introgressed DNA. However, this role is usually thought of as a direct one: a mating preference for conspecifics reduces the sexual fitness of hybrids, reducing the transmission of introgressed ancestry. Here, we explore a second, indirect role of mate choice as a barrier to gene flow. Under assortative mating, parents covary in their ancestry, causing ancestry to be "bundled" in their offspring and later generations. This bundling effect increases ancestry variance in the population, enhancing the efficiency with which post-zygotic selection purges introgressed DNA. Using whole-genome simulations, we show that the bundling effect can comprise a substantial portion of mate choice's overall effect as a postzygotic barrier to gene flow, and that it is driven by ancestry covariances both between and within maternally and paternally inherited genomes. Using estimates of the strength of assortative mating in avian hybrid zones, we calculate that the bundling effect of mate choice may increase the amount of purging of introgressed DNA by 40-80%, contributing substantially to the genetic isolation of species.

Utilization and Conservation of Landrace Chickens of Nigeria: Physical and Performance Characteristics, Issues and Concerns

The Nigerian indigenous chickens (NICs) are a critical component of the global animal genetic resources. They are distributed in rural areas, kept by the majority of the rural poor. They constitute different strains, or ecotypes local to tribes, regions, or ecological zones and are valued for their disease resistance, adaptation, and yield of valuable products and income on marginal inputs making them a low risk species. They are hence a unique and vital genetic resource and gene pool for present and long-term genetic improvement and human need for food and sustenance. The NIC is however; threatened by extinction owing to neglect, negative selection, breed substitution, and genetic introgression. There is need to draw research and policy attention to the conservation of NICs in accord with the global effort for the conservation of indigenous chickens which is probably the most neglected among farm animal species. The present review therefore, focuses on the physical and performance characteristics, genetic diversity and improvement, utilization and conservation of NIC genetic resources.

Taxonomic revision of south-eastern Australian giant burrowing frogs (Anura: Limnodynastidae: Heleioporus Gray)

The rarely encountered giant burrowing frog, Heleioporus australiacus, is distributed widely in a variety of sclerophyll forest habitats east of the Great Dividing Range in south-eastern Australia. Analyses of variation in nucleotide sequences of the mitochondrial ND4 gene and thousands of nuclear gene SNPs revealed the presence of two deeply divergent lineages. Multivariate morphological comparisons show the two lineages differ in body proportions with > 91% of individuals being correctly classified in DFA. The two lineages differ in the number and size of spots on the lateral surfaces and the degree by which the cloaca is surrounded by colour patches. The mating calls are significantly different in number of pulses in the note. The presence of a F2 hybrid in the area where the distribution of the two taxa come into closest proximity leads us to assign subspecies status to the lineages, as we have not been able to assess the extent of potential genetic introgression. In our sampling, the F2 hybrid sample sits within an otherwise unsampled gap of ~90km between the distributions of the two lineages. The nominate northern sub-species is restricted to the Sydney Basin bioregion, while the newly recognised southern subspecies occurs from south of the Kangaroo Valley in the mid-southern coast of New South Wales to near Walhalla in central Gippsland in Victoria. The habitat of the two subspecies is remarkably similar. Adults spend large portions of their lives on the forest floor where they forage and burrow in a variety of vegetation communities. The southern subspecies occurs most commonly in dry sclerophyll forests with an open understory in the south and in open forest and heath communities with a dense understory in the north of its distribution. The northern subspecies is also found in dry open forests and heaths in association with eroded sandstone landscapes in the Sydney Basin bioregion. Males of both taxa call from both constructed burrows and open positions on small streams, differing from the five Western Australian species of Heleioporus where males call only from constructed burrows. Using the IUCN Red List process, we found that the extent of occupancy and area of occupancy along with evidence of decline for both subspecies are consistent with the criteria for Endangered (A2(c)B2(a)(b)).

Hybridization with mountain hares increases the functional allelic repertoire in brown hares

Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.

Insights on the historical biogeography of Philippine native pigs and its relationship with Continental domestic and wild boars

The Philippine archipelago was believed to have never been connected to the Asian continent, even during the severe Quaternary sea-level drops. As a result, the history of pig dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with some human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine native pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boars corresponding to their geographic origin. Results revealed a considerable genetic diversity (0.900±0.016), and a widespread Asian pig-ancestry (94.60%) were revealed in the phylogenetic analysis with admixed European pig-origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close genetic connection between the continental wild boars and domestic pigs present in the Philippine pigs corroborates our hypothesis of a genetic signal that could potentially be associated with the recently reported multiple waves of human migrations to the Philippines during the last 50,000 years. The high frequency of haplotypes (54.08%) that collapsed in the D7 haplogroup represent an interesting challenge as its distribution does not coincide with the hypothesized migratory route of the Neolithic Austronesian-speaking populations. We detected the first Pacific Clade signature and ubiquitously distributed D2 haplotypes which postulate the legitimate dispersal of pigs associated with the multiple waves of human migrations involving the Philippines. The multimodal mismatch and neutrality test statistics both Fu’s Fs and Tajima’s D correlates the long stationary period of effective population size revealed in the Bayesian skyline plot. While the sudden decrease in population was consistent with the pronounced population bottleneck of Asian and European pigs during the interglacial periods of the Pleistocene.