Levels Of Heterozygosity Research Articles

Detecting hybridization in Chilean species of the genus Baccharis L.

The genus Baccharis in Chile is an extraordinary example of admixture, previously described only morphologically and chemically. In Chile, the genus forms a homoploid complex with at least 16 species and 21 hybrids. Genotyping-by-Sequencing (GBS) was used to clarify the hybrid character of Baccharis × intermedia, which originated from the species B. macraei and B. linearis. Additionally, B. vernalis, another species with a morphological resemblance to B. macraei, was subjected to analysis to ascertain its role in the hybridization process. A total of 11,006 SNPs and 72 individuals were analysed using Treemix, D- and f-statistics, which revealed genetic evidence of hybridization between B. macraei and B. linearis. Furthermore, other genetic indicators, such as a high level of heterozygosity, also provided evidence of the hybrid nature of Baccharis × intermedia. Additionally, one individual exhibited strong genetic proportions derived from B. vernalis, B. macraei, and B. linearis. Distinct individuals were clustered using sparse Non-Negative Matrix Factorization (sNMF) into five distinct groups, representing the described species and the hybrid. B. macraei exhibited division into a northern and a southern subpopulation. The morphological and chemical evidence of the hybrid character of Baccharis × intermedia is corroborated by genetic data. Further, the most likely evolutionary scenario is a hybrid swarm. Genetic differentiation between B. linearis and B. macraei indicates separation prior to secondary contact. The close relationship of B. macraei and B. vernalis was confirmed, suggesting that it may emerge as a vicariant species on different soil types.

Evolutionary genomics of Leishmania braziliensis across the neotropical realm

The Neotropical realm, one of the most biodiverse regions on Earth, houses a broad range of zoonoses that pose serious public health threats. Protozoan parasites of the Leishmania (Viannia) braziliensis clade cause zoonotic leishmaniasis in Latin America with clinical symptoms ranging from simple cutaneous to destructive, disfiguring mucosal lesions. We present the first comprehensive genome-wide continental study including 257 cultivated isolates representing most of the geographical distribution of this major human pathogen. The L. braziliensis clade is genetically highly heterogeneous, consisting of divergent parasite groups that are associated with different environments and vary greatly in diversity. Apart from several small ecologically isolated groups with little diversity, our sampling identifies two major parasite groups, one associated with the Amazon and the other with the Atlantic Forest biomes. These groups show different recombination histories, as suggested by high levels of heterozygosity and effective population sizes in the Amazonian group in contrast to high levels of linkage and clonality in the Atlantic group. We argue that these differences are linked to strong eco-epidemiological differences between the two regions. In contrast to geographically focused studies, our study provides a broad understanding of the molecular epidemiology of zoonotic parasites circulating in tropical America.

Population Genetics and Gene Flow in Cyphotilapia frontosa and Cyphotilapia gibberosa Along the East Coast of Lake Tanganyika

The radiation of cichlid species in the East African Great Lakes is remarkable and rapid. The population genetics of two deep-water Cyphotilapia species along the east coast of Lake Tanganyika from Burundi to southern Tanzania was determined using ddRAD-seq. A combination of ADMIXTURE, PCA, genome polarization, and 2D site frequency spectrum analyses confirmed the presence of two species, C. frontosa in the north and C. gibberosa in the south, as documented in other studies. We also found evidence of a potential hybrid zone connecting the two species at a sharp genetic cline centered in the middle of the lake and apparent introgression in both directions, but predominantly from ‘gibberosa’ into ‘frontosa’. The highest proportion of introgressed ‘gibberosa’ ancestry was present in the southernmost populations of C. frontosa collected near Karilani Island and Cape Kabogo. At the intra-specific level, there was support for between 1 and 3 populations of C. frontosa, whereas the results indicated only a single homogeneous population of C. gibberosa. The presence of different morphs in the lake despite the low levels of heterozygosity suggests that a small number of loci may be involved in the morphological variation and/or that there is a more complex interplay between genetics and the environment in different locations.

Survey sequencing and flow cytometry reveal the genomic characteristics and genetic markers of six wild sweetpotato species.

The lack of genomic and genetic research on wild sweetpotato species has hindered the advancement of sweetpotato variety development through modern crop improvement techniques. To facilitate the use of genomic and genetic approaches in sweetpotato variety development, we conducted a comprehensive assessment of the genome size and ploidy of six closely related wild sweetpotato species using flow cytometry and chromosome counting. Additionally, we acquired insights into their genomic characteristics through high-throughput sequencing. Based on the 17-mer frequency distribution, the genome sizes of these species ranged from 518.47Mb to 1,505.04Mb. Notably, most diploid species exhibited genome sizes of approximately 500Mb, with the diploid wild species I. purpurea standing out as having a significantly larger genome size compared to other diploid species. A substantial proportion of repeats (ranging from 57.47 to 81.07%) was identified across the genomes of the six species. Heterozygosity levels varied from 0.24 to 2.21%. SSR analysis revealed that the distribution of microsatellite patterns was largely consistent among the genomes of I I. lacunosa, I. tenuissima, and I. tiliacea, with mono-, di-, and trinucleotide motifs dominated by A/T, AT/AT, and AAT/ATT, respectively, indicating a strong A/T base preference. SNPs in this study were unevenly distributed across chromosomes, and non-synonymous SNVs in exonic accounted for 3.199% of the total number of SNPs, which may lead to genetic functional variation between species. In addition, the cross-regional annotation of SNPs highlights the diversity of gene regulatory regions and may provide insights into gene regulation, the underlying genetics of complex traits, and genetic differences between species. The current data reinforce the established positive correlation between genome size and ploidy in the genus Ipomoea. In particular, the diploid I. purpurea had a larger genome compared to other diploid species. The genome survey indicated that I. lacunosa(2x), I. tiliacea(2x), and I. tenuissima(2x) possess simple genomes with low heterozygosity (0.36%, 0.37%, and 0.24%, respectively). In contrast, I. purpurea(2x) has a simple genome but exhibits high heterozygosity (1.95%), while I. tabascana(4x) and I. trifida(6x) have complex genomes with high heterozygosity (2.21% and 1.54%, respectively). These results provide a reasonable basis for the selection of whole genome sequencing strategies for these species and would provide references for research into the genetic diversity of wild relatives of sweetpotato.

Genetic diversity, population structure, and phylogeny of insular Spanish pepper landraces (Capsicum annuum L.) through phenotyping and genotyping-by-sequencing.

Pepper (Capsicum spp.) is one of the most important crops worldwide. Understanding the species' genetic background is key to preserve agrodiversity on-farm, to contribute to a more diverse and resilient agrifood sector, and to find new sources of variation that could be useful in future breeding programs. In this regard, varietal groups bred in insular environments have gained special interest as they have evolved quite isolated from continental forms, with a limited genetic exchange. The present work explores the diversity of a plethora of Balearic landraces, corresponding to different local varietal types, through phenotyping and genotyping-by-sequencing (GBS). Mallorca and Eivissa landraces were phenotyped according to a comprehensive list of descriptors for plant, leaf, flower, fruit, pollen, and seed and were genotyped with single nucleotide polymorphism (SNP) markers; population structure and their patterns of diversity were studied. The results showed a considerable morphological diversity for most traits analyzed, within and between landraces. On the whole, in regard to genetic patterns, relatively low levels of heterozygosity and moderate genetic diversity for the studied landraces were found although some of them exhibited diverse patterns. The materials were not grouped in specific clusters associated with each island, but mainly according to varietal types. These findings can serve as the basis for studying divergent evolutionary patterns associated with the corresponding populations. Finally, the results can contribute to further elucidation of the genetic basis of Balearic landraces and serve as an inspiring case of study for other insular endemisms of cultivated species.

Genetic Characterization of Procambarus clarkii Cultured in Sichuan Province Based on Microsatellite Markers

The Procambarus clarkii production sector in Sichuan Province, China, is experiencing rapid growth. However, the industry faces significant challenges, including on-farm breeding and the widespread “Catch Big, Keep Small” farming practice, which have led to substantial genetic degradation within P. clarkii populations. Moreover, the uncertainty surrounding the origins of breeding stocks poses an additional obstacle to the local selection and cultivation of high-quality juvenile P. clarkii. With the objective of inferring the genetic lineage of cultivated P. clarkii in Sichuan, twelve microsatellite loci were employed to investigate the genetic characters of six P. clarkii populations from Sichuan and two from Hubei Province, China. The results revealed that the Sichuan populations exhibited higher levels of heterozygosity (Ho = 0.549~0.699, He = 0.547~0.607) and genetic diversity than the Hubei populations (Na = 4.00~5.250, PIC = 0.467~0.535). Notably, the DY population located in northeastern Sichuan showed the highest heterozygosity (Ho = 0.699, He = 0.607) and genetic diversity (Na = 5.250, PIC = 0.535) among the eight populations. Population structure, principal coordinate analysis and clustering analysis illuminated a close genetic relationship between the Qionglai population in Sichuan and the Jianli population in Hubei. Additionally, the remaining five Sichuan populations (Luxian, Nanxi, Xingwen, Neijiang and Daying) exhibited strong genetic affinity with the QianJiang population in Hubei, and particularly high genetic exchange may have occurred between Daying and Qianjiang (Fst = 0.001, Nm = 217.141). These results suggest that the primary cultivated P. clarkii populations in Sichuan likely originated from Qianjiang and Jianli counties in Hubei, with Qianjiang contributing a more substantial proportion. The genetic diversity of Sichuan populations was higher than those of some other Chinese P. clarkii farming provinces and even some native populations. Specifically, the Daying population emerges as a potential breeding germplasm source for crayfish in Sichuan. In contrast, the Qionglai population exhibits relatively low genetic diversity, highlighting the need for strategic enhancement through interactions with other populations to promote diversity and resilience. Furthermore, fostering genetic exchange among locally cultivated populations within the southern Sichuan basin is strategic to elevate the quality of P. clarkii germplasm resources.

Genetic structure of cattle of the siberian branch by microsatellite loci

Molecular-genetic methods are essential tools for the utilization and conservation of animal genetic resources. These methods facilitate more efficient management and control of breeding programs within livestock production systems. For studying the genetic diversity of a population, the use of STR markers is relevant due to the high variability of repeats. This study presents a genetic characterization of a Holstein and Black Pied cattle population (n = 10233) in Western Siberia using 12 microsatellite loci (BM1818, BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA126, TGLA122, TGLA227, TGLA53). A total of 145 alleles were identified across all loci, with frequencies ranging from 0.00005 to 0.68961. The highest level of genetic diversity was observed at the TGLA122 locus (25 alleles) with an average number of effective alleles (Ne) of 4.5. The least polymorphic locus was BM1824 (7 alleles) with an average Ne of 3.27. The average observed (Ho) and expected (He) heterozygosity across all loci was 0.6. The highest variability was observed at the TGLA53 locus, with a Wright’s fixation index (Fis) of 0.161, indicating a heterozygote deficiency. A similar deficiency was observed at the BM1818 locus. All other loci exhibited a positive Fis, with the highest value observed at the ETH3 locus (-0.074), indicating an excess of heterozygotes. The average Fis across all loci was -0.02, suggesting a sufficient level of heterozygosity within the studied population. These findings provide valuable information for population studies and practical breeding programs aiming to manage genetic diversity and improve selection efficiency in this cattle population.

Identification of the genetic background of laboratory rats through amplicon-based next-generation sequencing for single-nucleotide polymorphism genotyping

BackgroundLaboratory rats, as model animals, have been extensively used in the fields of life science and medicine. It is crucial to routinely monitor the genetic background of laboratory rats. The conventional approach relies on gel electrophoresis and capillary electrophoresis (CE) technologies. However, the experimental and data analysis procedures for both of these methods are time consuming and costly.ResultsWe established a single-nucleotide polymorphism (SNP) typing scheme using multiplex polymerase chain reaction (PCR) and next-generation sequencing (NGS) to address the genetic background ambiguity in laboratory rats. This methodology involved three rounds of PCR and two rounds of magnetic bead selection to improve the quality of the sequencing data. We simultaneously analysed 100 laboratory rats (including rats of 5 inbred strains and 2 in-house closed colonies), and the sequencing depth varied from an average of 108.25 to 5189.89, with sample uniformity ranging from 82.5 to 97.5%. A total of 98.9% of the amplicons were successfully genotyped (≥ 30 reads). Genetic background analysis revealed that all 38 experimental rats from the 5 inbred strains were successfully identified (without a heterozygous allele). For the 2 in-house closed colonies, the average heterozygosity (0.162 and 0.169) deviated from the typical range of 0.5–0.7, indicating a departure from the ideal heterozygosity level. Additionally, we employed multiplex PCR-CE to validate the NGS-based method, which yielded consistent results for all the rat strains. These results demonstrated that this approach significantly improves efficiency, saves time, reduces costs and ensures accuracy.ConclusionBy utilizing NGS technology, our developed method leverages SNP genotyping for genetic background identification in laboratory rats, demonstrating advantages in terms of labour efficiency and cost-effectiveness, thereby rendering it well suited for projects involving extensive sample cohorts.

Взаимосвязь геномного и расчетного инбридинга в популяции крупного рогатого скота голштинской породы Свердловской области

Abstract. The purpose of this paper is to study the inbreeding change of Holstein cattle in Sverdlovsk region and to show the correlation between genomic and estimated inbreeding. Methods. The study was conducted in six farms of the Sverdlovsk region and included 512 cows and heifers with date of birth from 2007 to 2022 and 12 breeding bulls. Chips GGP Bovine 150K (Neogen, USA) and Bovine 50K (Illumina, USA) were used for genotyping. Genome inbreeding estimates F were conducted with --het function in PLINK v1.9. Homozygosity inbreeding coefficient FROH was calculated with “sliding window” package of detectRUNS; FPED was taken from SELEX database, where it was calculated by pedigrees with Wright-Kislovsky formula. Scientific novelty. The comparison of genomic inbreeding for different age groups and estimation of correlations with pedigree inbreeding was conducted in Sverdlovsk region for the first time. Results. Our studies show that inbreeding coefficients increase radically from younger to older age groups. Holstein breed bulls show the highest value of inbreeding. At the same time heterozygosity level, estimated with sMLH tends to decrease with age. In addition, a strong correlation between estimated by pedegree inbreeding FPED and date of birth, as well as weak correlations between FPED and genomic coefficients (which have strong correlations with each other) were established.

Genetic Diversity, Kinship, and Polychromatism in the Spotted Eagle Ray Aetobatus ocellatus of Fiji

The spotted eagle ray Aetobatus ocellatus (Kuhl, 1923) has a widespread Indo-West Pacific distribution and displays substantial population genetic structuring. Genetic data are crucial for understanding the species’ diversity, connectivity, and adaptation. However, molecular genetic information on A. ocellatus from Melanesia is lacking, which impedes our understanding of gene flow among geographic regions. In this study, we sampled 45 A. ocellatus, primarily from Fiji’s largest fish market in the capital, Suva. Mitochondrial DNA Cytochrome C Oxidase subunit I (COI) barcoding was used for species identification, and DArT-seqTM technology was applied to assess the nuclear genetic diversity. Barcoding of the COI gene showed a 98.6% to 99.8% similarity to A. ocellatus reference sequences in the Barcode of Life Data System, and the 45 individuals were represented by three major evolutionary haplotype clusters. Genotyping resulted in 24,313 Single-Nucleotide Polymorphisms (SNPs) which were quality-filtered to 7094 SNPs per individual. The observed heterozygosity level was 0.310. The inbreeding coefficient was positive, and genotyping identified one full-sibling pair and one half-sibling pair from the 45 individuals. Additionally, eagle rays exhibit polychromatic patterns, and at least three ventral pattern variations were recorded in specimens from the market. Collectively, our main findings characterize the genetic profile of A. ocellatus in Fiji and can help to understand the diversification of this species within the region.

Analysis of inbreeding depression in five S1 Cassava families of elite varieties at the seedling nursery and clonal evaluation trial stages.

Background Cassava is an outcrossing, highly heterozygous plant that is reported to suffer from inbreeding depression. However, unraveling recessive traits and exploring additive genes would require a limited level of inbreeding for the genetic improvement of cassava. Method The impact of inbreeding depression (ID) on agronomic and biotic tolerance of cassava was evaluated using the S1 progenies of five African cassava varieties (TMS 30572, TME 419, TMS 98/0505, TMS 01/1371, and TMS 98/0002) at the seedling and clonal evaluation stages. Results At both trial stages, the effects of ID were severe on average performance of fresh root yield and fresh foliage yield; moderate on harvest index, dry matter content, vigor, and tolerance to cassava mosaic disease, cassava bacterial blight, and cassava anthracnose diseases; and less severe on plant height. Further examination of S1 families using molecular markers showed varying levels of heterozygosity at several loci across the genome. In addition, the degree of heterozygosity and ID varied by the S1 family. The TMS 01/1371 family showed the lowest degree of heterozygosity and ID on the average performance of different agronomic attributes, indicating that inbreeding may be strategically explored in this family to increase genetic gain and identify useful recessive traits. Lastly, the observed depression from inbreeding was higher in seedling evaluation than in clonal evaluation trials for fresh root yield, fresh foliage yield, harvest index, and dry matter content. Conclusion S1 individuals showing relatively low heterozygosity based on SNP data were selected as parents to advance genetic gain in cassava. Generally, reduced heterozygosity was prominent in traits with severe ID impacts on average phenotypic performance. Our results highlight the relative importance of exploring non-additive genetic effects and transgressive segregations for favorable allele combinations in cassava improvement.

Assessment of genetic diversity and population structure of U.S. Polypay sheep from breed origins to future genomic selection.

Knowledge of past and present genetic diversity within a breed is critical for the design and optimization of breeding programs as well as the development of strategies for the conservation of genetic resources. The Polypay sheep breed was developed at the U.S. Sheep Experiment Station (USSES) in 1968 with the goal of improving productivity in Western U.S. range flocks. It has since flourished in the more intensively managed production systems throughout the U.S. The genetic diversity of the breed has yet to be documented. Therefore, the primary objective of this study was to perform a comprehensive evaluation of the genetic diversity and population structure of U.S. Polypay sheep using both pedigree- and genomic-based methods. Pedigree data from 193 Polypay flocks participating in the National Sheep Improvement Program (NSIP) were combined with pedigree records from USSES (n = 162,997), tracing back to the breed's origin. A subset of these pedigreed sheep from 32 flocks born from 2011 to 2023 were genotyped with the GGP Ovine 50K BeadChip containing 51,867 single nucleotide polymorphisms (SNPs). Four subgroups were used for the pedigree-based analyses: 1) the current generation of animals born in 2020-2022 (n = 20,701), 2) the current generation with a minimum of four generations of known ancestors (n = 12,685), 3) only genotyped animals (n = 1,856), and 4) the sires of the current generation (n = 509). Pedigree-based inbreeding for the full population was 2.2%, with a rate of inbreeding of 0.22% per generation. Pedigree-based inbreeding, Wright's inbreeding, and genomic inbreeding based on runs of homozygosity were 2.9%, 1.3%, and 5.1%, respectively, for the genotyped population. The effective population size ranged from 41 to 249 for the pedigree-based methods and 118 for the genomic-based estimate. Expected and observed heterozygosity levels were 0.409 and 0.403, respectively. Population substructure was evident based on the fixation index (FST), principal component analysis, and model-based population structure. These analyses provided evidence of differentiation from the foundation flock (USSES). Overall, the Polypay breed exhibited substantial genetic diversity and the presence of a population substructure that provides a basis for the implementation of genomic selection in the breed.

High conservation importance of range-edge populations of Hooded Vultures (Necrosyrtes monachus)

Critically endangered Hooded Vultures (Necrosyrtes monachus Temminck, 1823), like many vulture species globally, are experiencing rapid population declines due to anthropogenic factors such as poisonings, human persecution, trading for belief-based use, and habitat loss/degradation. The Hooded Vulture is widespread across sub-Saharan Africa. Although it is considered one of the most abundant vultures in West Africa, this vulture species is less common in East and southern Africa, with the population at the southern-most edge of the distribution (in South Africa and Eswatini) estimated at only 100–200 mature individuals. The distribution of Hooded Vultures has contracted dramatically in southern Africa, with breeding populations largely confined to protected areas such as the Greater Kruger National Park. This study aimed to investigate the genetic diversity of the southern African range-edge population and assess if the recent contraction in the distribution has resulted in the population experiencing a genetic bottleneck. Sixteen microsatellite loci were amplified for samples collected along the Olifants River in the Greater Kruger National Park (n = 30). The genetic diversity in the South African population was compared to samples (n = 30) collected in Ghana, where Hooded Vultures are more abundant. Contrary to expectations, the South African peripheral Hooded Vulture population showed higher levels of heterozygosity (HO = 0.495) than the Ghanaian population (HO = 0.315). Neither population showed signs of recent bottleneck events when tested using demographic modelling and Approximate Bayesian computation (ABC). However, both populations showed high levels of inbreeding and relatedness. Our results suggest that despite being a small peripheral population, the South African Hooded Vulture population showed a similar level of genetic diversity as individuals sampled from a core population within the species distribution (in Ghana). This study supports the need for Hooded Vulture conservation efforts in the southern African region and highlights the evolutionary importance of range-edge populations.

Comprehensive genetic analysis reveals the genetic structure and diversity of Calanthe hoshii (Orchidaceae), an endemic species of the Ogasawara Islands: Implications for appropriate conservation of a critically endangered species

AbstractThe Ogasawara Islands, isolated from the continent throughout their geological history, harbor abundant endemic species. However, 32% of the native plant species are on the Japanese Red List, signaling their endangered status. Among these endangered species, Calanthe hoshii stands out as highly susceptible to extinction. Two wild and 89 ex situ individuals were alive in 2020, but the last known wild individual died in October 2021, indicating this species may have become extinct in the wild. Despite the conservation efforts under the Act for the Conservation of Endangered Species of Wild Fauna and Flora, the lack of essential information regarding genetic diversity and population structure among the remaining individuals poses a significant obstacle to developing effective conservation measures. In this research, we conducted a genetic analysis of the wild and ex situ individuals, which revealed notably reduced genetic diversity between individuals, with individual heterozygosity levels (1.0 × 10−5) measuring one‐ninth of those observed within a closely related species Calanthe triplicata (1.5 × 10−4). Comprehensive genetic analysis revealed that C. hoshii consisted of three genetic clusters of different sizes: cluster 1 comprised 95% of the total population, while clusters 2 and 3, with few individuals, were only found in the ex situ populations at Koishikawa Botanical Garden. Since extant C. hoshii maintains a remarkably low genetic diversity at both individual and population levels, it is necessary to consider future management strategies, such as artificial breeding among different clades identified in this study, to safeguard the stability and resilience of this species.

Spatial variation in genomic signatures of local adaptation during the cane toad invasion of Australia.

Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north-central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic-environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post-introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories.

Evidence for human-caused founder effect in populations of Solanum jamesii at archaeological sites: II. Genetic sequencing establishes ancient transport across the Southwest USA.

The domestication of wild plant species can begin with gathering and transport of propagules by Indigenous peoples. The effect on genomic composition, especially in clonal, self-incompatible perennials would be instantaneous and drastic with respect to new, anthropogenic populations subsequently established. Reductions in genetic diversity and mating capability would be symptomatic and the presence of unique alleles and genetic sequences would reveal the origins and ancestry of populations associated with archaeological sites. The current distribution of the Four Corners potato, Solanum jamesii Torr. in the Southwestern USA, may thus reflect the early stages of a domestication process that began with tuber transport. Herein genetic sequencing (GBS) data are used to further examine the hypothesis of domestication in this culturally significant species by sampling 25 archaeological and non-archaeological populations. Archaeological populations from Utah, Colorado and northern Arizona have lower levels of polymorphic loci, unique alleles, and heterozygosity than non-archaeological populations from the Mogollon region of central Arizona and New Mexico. Principle components analysis, Fst values, and structure analysis revealed that genetic relationships among archaeological populations did not correspond to geographic proximity. Populations in Escalante, Utah were related to those on the Mogollon Rim (400 km south) and had multiple origins and significant disjunctions with those populations in Bears Ears, Chaco Canyon, and Mesa Verde sites. Movement of tubers from the Mogollon region may have occurred many times and in multiple directions during the past, resulting in the complex genetic patterns seen in populations from across the Four Corners region.

Genetic prospective of a local invader: the strange pattern of Pontastacus leptodactylus population structure in Greece and Turkey based on microsatellite DNA.

The combination of the increasing demand of freshwater crayfish exports, the reduced population sizes due to overfishing, the crayfish plague epidemics and the habitat degradation, have led to unrecorded translocations of Pontastacus leptodactylus in Greek lakes. In the present study, the genetics of five narrow clawed crayfish (P. leptodactylus) populations were studied, namely three translocated populations inhabiting in Northern Greece, one native Greek population from Evros river and one potential progeny source population from Turkey. Nine microsatellite loci previously designed for the specific species were investigated, in order to assess the levels of genetic diversity and further to confirm the origin of these translocated populations some decades after the translocation events. Our results confirmed that the source population for the translocated Greek population is the Turkish lake Eğirdir. Further, despite the low values of the number of alleles, heterozygosity, and FST the populations were generally diverse, providing evidence for local adaptation. The low values of FIS for the translocated populations in combination with the high values of gene flow, possibly indicate the existence of re-introducing events. Apart from the translocated populations, high levels of genetic diversity and heterozygosity were observed in Evros population, suggesting it as a possible unit for future conservation purposes both as a donor population for reintroduction purposes as well as a unique gene pool protection source. To the best of our knowledge this is the first study dealing with the genetic composition of Greek P. leptodactylus populations from Nothern Greece, operating as a first step towards the development of proper management practices for restocking events and monitoring of translocated populations.

Microsatellite polymorphism based genetic variation in two sympatric species of Drosophila: D.bipectinata and D. malerkotliana

Drosophila bipectinata and D. malerkotliana are found to be distributed all along the Oriental-Australian continents and have common phylogenetic descent. The genetic divergence of these two species have been studied by using genetic markers like chromosome inversions and allozyme variants to establish the extent of variation they have experienced since their speciation. In this study, microsatellite variations have been considered to observe the genetic differentiation among the seven natural populations of D. bipectinata and six populations of D. malerkotliana. Results pertaining to both the species indicate that the level of average heterozygosity increases from north to south. Distinct genetic differentiation has been observed between north and south populations of both the species giving an indication that north and south populations have undergone genetic structuring due to absence of gene flow between them and varying environmental conditions. Based on the frequencies of microsatellite variants of the two species, we have computed the level of variation between these two species. The analysis in this regard shows an almost similar trend of genetic variation being experienced by these two species which could be a kind of parallel evolution occurring due to similar ecological niches occupied by them and similar impact of evolutionary forces.

Use of ISSR markers for genotyping an experimental group of largemouth bass Micropterus salmoides (LACEPEDE, 1802), reared in ponds of Polissia of Ukraine

The aim of this study was to investigate the genetic structure of the experimental group of largemouth bass reared in the ponds of Polissia of Ukraine using ISSR markers. To accomplish these tasks, ISSR genotyping of the genetic structure of largemouth bass was performed using four fragments of trinucleotide loci. The genetic structure of the experimental group of largemouth bass of the pond fsh farm "Nyvka" was characterised using 4 primers B – (GAG)6C; C – (AGC)6G; D – (ACC)6G and E – (AGC)6C. Fins fragments were used for the study. In the course of the work, the optimal conditions for ISSR-PCR analysis were selected. The study revealed a number of factors that affect the efciency of these markers: DNA concentration, number of amplifcation cycles. For 4 markers, 80 alleles with a molecular weight of 160–1320 bp were identifed. The ranges of amplicons for the selected markers were determined: marker B – from 150 to 1186 bp; marker C – from 640 to 200 bp; D – from 1320 to 225 bp; and E – within 630–160 bp. The most polymorphic marker is marker B – 26 alleles, the least polymorphic marker is marker E – 15 alleles. In the studied experimental group of largemouth bass, the effective number of alleles varied from 10.2 for marker E to 12.2 for marker C, D. The indicators of genetic variability were determined by calculating allelic frequencies, the maximum level of available heterozygosity is 0.918 for marker C, D, and the lowest for marker E is up to 0.902. A method has been proposed that makes it possible to analyse the genetic structure of the experimental group of largemouth bass using these primers and to implement genetic information at different stages of the selection process. Keywords: ISSR-PCR, genetic structure, largemouth bass, DNA– markers, genotype, amplicons, genetic polymorphism, molecular genetic marker.

A comprehensive genome survey study unveils the genomic characteristics and phylogenetic evolution of fishes in the Uranoscopidae family

The construction of high-quality genomes is fundamental for molecular studies of species. Currently, there are no published genome sequences within the Uranoscopidae family, and research on the genomic characteristics of this family is lacking. In this study, genomic analyses of seven species from the Uranoscopidae family which captured from the southeastern coast of China were conducted using next-generation sequencing technology. The results revealed that the genomic characteristics of the seven species are relatively similar. The genome sizes of the seven Uranoscopidae species ranged from 536.00 Mb to 652.49 Mb, with repeat sequence proportions between 20.09% and 36.64%, and heterozygosity levels ranging from 0.41% to 0.88%. The assembled draft genomes exhibited GC contents of these species ranging from approximately 42.14% to 43.53%. Furthermore, the mitochondrial sequences for the seven species were assembled, with sizes ranging from 14,966 to 18,446 bp. The evolutionary relationships between different species were depicted through the mapping of conserved genes, whole-genome variances and mitochondrial genome sequences. Besides, the historical effective population sizes of all species experienced rapid expansion after the Last Interglacial Period, with three species undergoing bottleneck effects. In conclusion, this study provides a reference for the subsequent construction of high-quality genomes for species within the Uranoscopidae family and offers a rich data resource for further evolutionary research.