Single Genetic Group Research Articles

Indigenous Australian genomes show deep structure and rich novel variation

The Indigenous peoples of Australia have a rich linguistic and cultural history. How this relates to genetic diversity remains largely unknown because of their limited engagement with genomic studies. Here we analyse the genomes of 159 individuals from four remote Indigenous communities, including people who speak a language (Tiwi) not from the most widespread family (Pama–Nyungan). This large collection of Indigenous Australian genomes was made possible by careful community engagement and consultation. We observe exceptionally strong population structure across Australia, driven by divergence times between communities of 26,000–35,000 years ago and long-term low but stable effective population sizes. This demographic history, including early divergence from Papua New Guinean (47,000 years ago) and Eurasian groups1, has generated the highest proportion of previously undescribed genetic variation seen outside Africa and the most extended homozygosity compared with global samples. A substantial proportion of this variation is not observed in global reference panels or clinical datasets, and variation with predicted functional consequence is more likely to be homozygous than in other populations, with consequent implications for medical genomics2. Our results show that Indigenous Australians are not a single homogeneous genetic group and their genetic relationship with the peoples of New Guinea is not uniform. These patterns imply that the full breadth of Indigenous Australian genetic diversity remains uncharacterized, potentially limiting genomic medicine and equitable healthcare for Indigenous Australians.

Exploring the Genetic Diversity and Population Structure of Daphnia cucullata Sars, 1862 in Boreal Lakes (Latvian Lakeland) Based on Microsatellites

We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most appropriate microsatellite markers for future genetic studies of Daphnia cucullata populations of lakes Svente, Riča, Dridzis and Geraņimovas-Ilzas in the Boreal biogeographical region. Based on these microsatellite markers, we determined the genetic diversity of these populations. The loci Dgm105 and Dgm101 had the maximum number of alleles and the maximum number of private alleles. The specific locus Dgm105 had five private alleles (62% of all detected alleles), and locus Dgm101 had four private alleles (57% of all detected alleles) in these loci. We determined the observed heterozygosity (Hobs) and the expected heterozygosity (Hexp) level (via Hardy–Weinberg equilibrium), the number of polymorphic loci, the number of detected alleles in each analyzed microsatellite locus, the average number of alleles at the locus (Na), the average effective number of alleles at the locus (Ne), the FST of the population’s genetic differentiation, the genetic distance (D) (following Nei) and the significance (χ2-test) of differences between the levels of observed and expected heterozygosity. It was shown that Daphnia cucullata populations from lakes with a low number of zooplankton taxa (Riča and Geraņimovas-Ilzas) have a higher genetic diversity compared to lakes with a high number of zooplankton taxa (Dridzis and Svente). It was found that Daphnia cucullata populations from lakes Dridzis and Svente have the least genetic distance, and these populations form a single genetic group, as confirmed via clustering.

Morphological and Genetic Identification of Harpacticella inopinata (Harpacticoida, Copepoda) from Lake Baikal and the Yenisei River (Russia)

The results of studies of the morphology and genetics of the Baikal subendemic (Harpacticella inopinata Sars, 1908 harpacticoid) are presented. The collections of 1969 and 2017–2022 from the southern part of Lake Baikal and the Yenisei River within the city of Krasnoyarsk are used as material. It is demonstrated that morphological variability within the species is most pronounced in the structure of the antenna exopodite and the number of pores and sensilla on the integument of thoracic somites. The genetic variability of the studied H. inopinata sample is described by three clades with an average distance between them of 0.24; genetic distances between individuals within the detected genetic groups do not exceed 0.005. It is found that H. inopinata from geographically distant habitats (Lake Baikal and the Yenisei River) form a single morphological and genetic group. The analysis of genetic diversity of H. inopinata confirms the relatively recent Baikal origin of the species in the Yenisei River, probably associated with an anthropogenic invasion.

Morphological and Genetical Identification of <i>Harpacticella inopinata</i> Sars (Harpacticoida, Copepoda) from Lake Baikal and the Enisey River

The work presents the results of comparative studies of the morphology and genetics of the Baikal subendemic – the harpacticoid copepod Harpacticella inopinata Sars, 1908. The material was obtained from the southern part of Baikal Lake and the Yenisei River within the of Krasnoyarsk city in 1969, 2017–2022. It is shown that morphological variability within the species appeared most in the structure of the antenna exopodite, the number of pores and sensillas on the integument of thoracic somites. The genetic variation of the studied sample of H. inopinata was described by four clades with a distance between them of 0.26, the genetic distances between individuals within the detected genetic groups did not exceed 0.005. It was determined that H. inopinata from geographically remote habitats (Baikal Lake and Yenisei River) forms a single morphological and genetic group. Analysis of the genetic diversity of H. inopinata confirms the relatively recent Baikal origin of the species in the Yenisei, probably associated with an anthropogenic moving into the river.

Lack of genetic structure in euryhaline Chelon labrosus from the estuaries under anthropic pressure in the Southern Bay of Biscay to the coastal waters of the Mediterranean Sea

Over the last decade, xenoestrogenic effects have been reported in populations of thicklip grey mullet Chelon labrosus from contaminated estuaries in the Bay of Biscay, resulting in intersex condition. To understand the level of gene flow in individuals of different Basque estuaries microsatellite markers were used to evaluate the population structure and connectivity of C. labrosus from estuaries of the Basque coast. 46 microsatellites were tested and 10 validated for the analysis of 204 individuals collected from 5 selected Basque estuaries and 2 outgroups in the Bay of Cadiz and Thermaic Gulf. The polymorphic microsatellites revealed 74 total alleles, 2–19 alleles per locus. The mean observed heterozygosity (0.49 ± 0.02) was lower than the expected one (0.53 ± 0.01). There was no evidence of genetic differentiation (FST = 0.0098, P = 0.0000) among individuals or sites. Bayesian clustering analysis revealed a single population in all sampled locations. The results of this study indicate widespread genetic homogeneity and panmixia of C. labrosus across the current sampling areas spanning the Atlantic and Mediterranean basins. The hypothesis of panmixia could therefore be well supported so individuals inhabiting estuaries with high prevalence of intersex condition should be considered as members of the same single genetic group as those inhabiting adjacent estuaries without incidence of xenoestrogenicity.

Population genomics reveals differences in genetic structure between two endemic arboreal rodent species in threatened cloud forest habitat

Genomic tools are now commonly used to assess the genetic diversity and genetic structure of species and populations, and they provide the ability to describe and address the negative effects of population declines and fragmentation. However, such studies are lacking for arboreal mammals despite their contribution to various ecosystem services, especially in uncommon and critically endangered ecosystems such as cloud forests. The aim of this work was to evaluate and compare the genetic diversity and population structure of two endemic arboreal mice from Mexican cloud forests that are associated with areas with different levels of impacts from human activities. We performed genotyping-by-sequencing in 47 Habromys schmidlyi and 17 Reithrodontomys wagneri individuals to evaluate genetic diversity and differentiation. In both species, the genetic diversity was low compared to other cricetid species, and we observed different population structure patterns, potentially linked to the different ecological associations. We detected two genetic groups in H. schmidlyi, that is a territorial species present in areas of low incline, while a single genetic group was found in R. wagneri, which forms family groups in areas with steep slopes. Overall, these results highlight how species’ genetic diversity can be differentially impacted depending on differential ecological associations within the same ecosystem. This information is essential for the development of the adequate conservation and management of these species.

The Influence of Genetic Ancestry on Disease Biology in Pediatric T-Cell Acute Lymphoblastic Leukemia

Introduction: Pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) is a biologically heterogenous disease that can be grouped into 16 subtypes based on integration of gene expression and somatic genomic alterations that have variable prevalence of activated targetable pathways (Pölönen P., et al ASH 2022). In both adult cancers and pediatric B-cell ALL, genetic ancestry has been associated with tumor biology and clinical outcomes; however, there is a paucity of data exploring the influence of genetic ancestry in T-ALL. Thus, we sought to determine the association of genetic ancestry with tumor biology in pediatric T-ALL. Methods: Whole genome sequencing (germline and tumor) and bulk RNA-sequencing was performed to characterize T-ALL subtype and pathway aberrations among 1312 newly diagnosed T-ALL patients treated on Children's Oncology Group trial AALL0434. Genetic ancestral composition was determined for each individual using the iAdmix program comparing allele frequencies between patients and reference genomes from the 1000 Genomes Project. Coefficients from the 5 reference populations (European (EUR), African (AFR), East Asian (EAS), South Asian (SAS), and American Admixture (AA)) were assumed to sum to 100%. Categorical genetic ancestral groups were classified from prior methods: "European" (EUR >90%), "African" (AFR >70%), "East Asian" (EAS >90%), "South Asian" (SAS >70%), and "Amerindian" (AA >10% and AA greater than AFR), with the rest defined as "Other." We evaluated associations of genetic ancestry with T-ALL molecular subtypes and pathways. Ancestry was first examined as a categorical variable using Fisher's exact test for its association with subtypes and pathways. Ancestry was also analyzed as a continuous variable using logistic regression for association with pathways and multinomial regression for association with subtype (TAL1-RB subtype as reference). The effect of ancestry was summarized as odds ratios (OR) for every 25% increase in a non-European ancestry, with a concurrent 25% decrease in European ancestry and remaining ancestries fixed. Results: Categorical ancestral composition in this cohort was 59% European, 11% African, 15% Amerindian, 3% East Asian, 2% South Asian, 10% Other. The prevalence of T-ALL subtypes differed by genetic ancestry (Figure 1). For example, HOXA9 and BCL11B, which are linked to ETP T-ALL, were significantly enriched in children of African genetic ancestry as compared to European ancestry (HOXA9: 11% AFR vs. 6% EUR; BCL11B: 3% AFR vs. 1.5% EUR). ETP phenotype was also more common in children of African descent as compared with European (11.9% vs. 7.5%, p =0.031). In analyses of ancestry as a continuous variable (with European as the reference), four subtypes and four pathways exhibited differences in odds of expression (Table 1). For every 25% increase in African ancestry, the odds of BCL11B subtype was 41% higher (p=0.034), odds of HOXA9 subtype was 26% higher (p=0.020), odds of MLLT10_TRA was 68% higher (p<0.001), and odds of tumor microenvironment (TME) aberrant subtype was 33% higher (p=0.027). For every 25% increase in African ancestry, patients were also 1.13-fold more likely to harbor JAK/STAT mutations (p=0.049) and 1.18-fold for MAPK/RAS pathway alterations (p=0.011), with decreasing odds of NOTCH mutations (OR=0.88, p=0.014) or ribosomal gene alterations (OR=0.69, p=0.003). For increasing East Asian ancestry, patients were also less likely to have NOTCH pathway alteration (OR=0.85, p=0.027), whereas there was no difference for increasing South Asian ancestry. Conclusion: Disease biology varies substantially among children of different genetic ancestries with T-ALL. Given that subtypes may inform future risk stratification, and pathways may guide novel treatment strategies, examining subtype and pathway expression for children of all ancestral backgrounds is critical. Important biological indicators of risk may be missed when studying patients of a single genetic ancestral group or when focusing on averages for the entire cohort without taking into consideration variation in genetic ancestry. Analyses of survival by genetic ancestry within genomic groups are ongoing. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Shall the Wild Boar Pass? A Genetically Assessed Ecological Corridor in the Geneva Region

Landscape fragmentation caused by road infrastructures represents a major threat to the genetic diversity of a region. The resulting genetic isolation between subpopulations may lead to consanguinity, and consequently to population collapse and extinction. However, the construction of wildlife crossings can help maintain connectivity. In the present paper, we evaluated the genetic spatial structuring of populations of wild boars (Sus scrofa) in three areas of the Geneva region connected by an ecological corridor. Those areas are cut off either by a highway that is crossed by a wildlife overpass or by an anthropized sector. Genetic profiling with 9 nuclear microsatellite markers yielded 61 single profiles, which allowed for clustering, parentage, and linkage disequilibrium analyses, uncovering the populations’ genetic structure. We also evaluated whether the genetic structure was affected by the sex of individuals. In our analyses, all individuals clustered into a single genetic group, suggesting that no structure limited significantly the gene flow in the region. However, a recent admixture indicated a potential increase in the gene flow between two of the subpopulations due to the wildlife overpass, while the other part of the ecological corridor was not or was only partially functional. Genetic distances between males were significantly higher than between females, although the role of sex remains unclear as to its influence on population genetics. Finally, in order to avoid a subregion becoming fully isolated, urbanization planning should consider this genetic evaluation and proceed with further monitoring, especially by focusing on species more sensitive to landscape fragmentation.

VARIABILIDAD GENÉTICA DE AISLADOS DE PRSV-p DE PAPAYO EN LA ZONA CENTRO DEL ESTADO DE VERACRUZ, MÉXIC

&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt; The &lt;em&gt;Potyvirus Papaya ringspot virus &lt;/em&gt;type P (PRSV-p) causes the papaya (&lt;em&gt;Carica papaya &lt;/em&gt;L.) ringspot disease, which causes damage to the plantations of this crop. In regions where there is movement of plant material and continuous production processes, there is greater genetic variability of this virus; such is the case of the State of Veracruz, Mexico, one of the main papaya producers in the country. &lt;strong&gt;Objective: &lt;/strong&gt;To analyze the genetic variability of isolates of PRSV-p, present in commercial papaya plantations in the central zone of the State of Veracruz. &lt;strong&gt;Methodology: &lt;/strong&gt;Leaves with differential symptoms of the disease were collected. The capsid protein (CP) coding region was amplified by RT-PCR to confirm the identity of the virus.&lt;strong&gt; &lt;/strong&gt;The sequences obtained were analyzed, aligned and a phylogenetic tree was obtained. &lt;strong&gt;Results: &lt;/strong&gt;The presence of PRSV-p was confirmed by RT-PCR. Through sequence analysis, high diversity was observed in the first 50 amino acids encoded in the N-terminal region of CP. In the phylogenetic tree, three viral genetic groups were obtained. The largest conserved sites of interest (even the WCIEN box and QMKAAA) were found near the C-terminal region of the CP.&lt;strong&gt; &lt;/strong&gt;100% homology was observed in the central and C-terminal region of the Ver75Co isolate, with respect to the consensus sequence&lt;strong&gt;.&lt;/strong&gt; &lt;strong&gt;Implications: &lt;/strong&gt;The results show the genetic diversity of the virus in the central zone of the state of Veracruz, which will allow genetic modifications to improve resistance in papaya plants. &lt;strong&gt;Conclusions: &lt;/strong&gt;There is genetic variability of PRSV-p in Veracruz, there are conserved sites of interest (WCIEN and QMKAAA) and changes in the N-terminal region, which includes the EK repetitive region and the DAG codon. These changes may be a genetic characteristic of the virus for adaptation. The Ver75Co isolate may be the point of change that gives rise to the other isolates of this work. The phylogenetic tree shows a single genetic group of the virus, which is distributed in three different clades.&lt;/p&gt;

Genetic characterization of remaining populations of paratecoma peroba, an endangered and endemic species of the atlantic forest

Background: The objective of this study was the genetic characterization of remaining populations of the species Paratecoma peroba occurring in fragments of the Atlantic Forest, by estimating parameters of diversity and genetic structure. The study was carried out in two forest fragments, the Atlantic Forest Environmental Education Pole (area 1) and the Pacotuba National Forest (area 2), where 93 adult trees were identified. Results: Ten Inter Simple Sequence Repeats (ISSR) primers were used in genotyping, obtaining 112 amplified bands with 87.5% polymorphism. The genetic diversity estimated for the populations from the Nei (H*) and Shannon (I*) indices was higher for area 1. For the joint data, moderate genetic diversity was observed, referring to the average values of 0.26 and 0.40, obtained for the H* and I* indices, respectively. Molecular variance analysis resulted in moderate differentiation between populations (Φ ST = 0.143), while gene flow analysis (N m = 6.69) revealed the occurrence of similar alleles between them. However, the predominance of a single genetic group in area 2, revealed from Bayesian approach, indicates that its genetic structure, possibly generated by the current scenario of fragmentation of the Atlantic Forest and the distancing of populations, affecting the contemporary gene flow. Conclusion: Despite the moderate genetic diversity of the species for the area 2 population, actions toward inclusion of seedlings obtained from seeds from neighboring fragments, including area 1, and the increase in the connectivity of forest fragments through ecological corridors, could assist in augmenting its genetic variation.

Comparative evaluation of the immune responses of seven chicken ecotypes to vaccination against Newcastle disease

Newcastle disease (ND) is a highly contagious viral disease of poultry with high mortality. The local velogenic viral pool of the ND strains influences its severity and occurrence. ND vaccination is the most feasible approach to control the disease. However, some ND-vaccinated groups within chicken populations are susceptible to velogenic ND infection developing outbreaks with marked pathological lesions and shedding of the virus. Vaccine strain-related factors as well as inadequate vaccine application and delivery methods during vaccination might explain the suboptimum ND vaccine efficacy. In this study, however, we propose that host factors may contribute to the suboptimal vaccine efficacy in vaccinated chickens. We, therefore, compared the immune response of five Ethiopian chicken ecotypes to ND immunization in the presence of two reference breeds (Fayoumi and Bovans). All chickens received initial immunization at age of 21 days with HB1 ND vaccine followed by two-times LaSota booster immunization at age 50 and 120 days. Subsequently, serum was collected fortnightly post-vaccination at age 35, 65, and 135 days for immune response analysis using the hemagglutination inhibition (HI) test. HIantibody was significantly higher at days 135 &gt; 65 &gt; 35 in each ecotype following the third, second, and first vaccination, respectively. The different chicken ecotypes had significant differences in HI antibody response to the ND vaccination. Accordingly, the HI titer was significantly higher in Jarso &gt; Cheffe &gt; Fayoumi &gt; Arsi &gt; Bovans &gt; Tepi &gt; Horro suggesting antibody titer and ND vaccine efficacy of the ND vaccine depends on host factors. Moreover, some chicken groups within each ecotype had low HI titer. Chicken ecotypes with weak immune responses may not completely clear the virus from their body; thus, they can serve as a reservoir host by maintaining the ND virus. We conclude that herd immunity level and blanket vaccination program based on the results of a single host genetic group can be misleading during developing and recommending a new vaccine. Hence, understanding the host determinant factors in the immune response during vaccination can lead to improved efficacy and protection against ND in chicken populations.

Contemporary genetic structure of walleye (Sander vitreus) reflects a historical inter-basin river diversion

River diversions can have unexpected biological consequences. In the mid-20th century, the upper Ogoki River in northern Ontario was diverted from its original Hudson Bay drainage to flow into the Great Lakes. Although walleye were present in both systems prior to the diversion, the Hudson Bay and Great Lakes watersheds had previously been separated since the early Holocene (7500–8500 years ago). We assessed the effects that this inter-basin diversion has had on the genetic structure of two formerly allopatric populations. We assessed the genetic structure and diversity of walleye in the Ogoki and Little Jackfish river systems and Lake Nipigon (number, distribution, and divergence of identified genetic groups) and quantified the contribution of fish from the historical population (Hudson Bay drainage Ogoki River) and Lake Nipigon to walleye in the Ogoki and Little Jackfish Rivers. Walleye from Ogoki Lake, the Ogoki River diversion through the Little Jackfish River, Lake Nipigon and Nipigon Bay were genotyped at 10 microsatellite loci. Significant genetic differences were detected among sampling locations: walleye from Ogoki Lake, presumably representing fish originally from the historical Ogoki River gene pool, were genetically similar to but statistically distinct from walleye within the diversion. Walleye from sample sites within the diversion and Ombabika Bay appear to form a single genetic group that is largely derived from the Ogoki watershed and differs significantly from walleye in Lake Nipigon and Nipigon Bay. Our findings confirm that the historical river diversion has had long-term effects on the genetic composition of contemporary walleye populations.

A28 Spatial spread of highly pathogenic avian influenza A (H5N8) virus in Italy, 2017–8

In winter 2016–7 the highly pathogenic avian influenza (HPAI) virus, H5N8 subtype, clade 2.3.4.4 group B, circulated extensively both in wild and domestic birds in Europe. Northern Italy was hit by three epidemic waves: the first in January–May 2017, the second in July–December 2017, and the latest in March 2018. To genetically characterize the viruses circulating in Italy we used the Illumina MiSeq platform to sequence the complete genome of representative viruses from each infected farm, for a total of 86 cases in poultry and 17 in wild birds. Maximum likelihood phylogenetic analyses performed using PhyML version 3.1 identified multiple viral introductions of distinct genotypes of HPAI H5N8 viruses in Italy at the beginning of the epidemic (January–February 2017). During the second epidemic wave a single genetic group originating from the virus A/wild duck/Poland/82A/2016 seemed to have been selected, further evolving into two different clusters, namely Italy-A and Italy-B. We identified four clusters of secondary outbreaks, the largest being the epidemic in the province of Brescia between October 2017 and March 2018, which had affected 26 farms. Evolutionary and phylogeographic analyses performed with the BEAST v1.8.4 package (applying a Bayesian Markov chain Monte Carlo approach, using a constant size coalescent tree prior and a SRD06 model of nucleotide substitution) indicated that different viral introductions had probably occurred through migratory birds from West Russia, Siberia, Central and East Europe. The discrete and continuous phylogeographic analyses showed that group Italy-A had probably emerged between February and April 2017 in the province of Mantua and had then spread eastwards, circulating in the Veneto region and eastern Lombardy; on the contrary, Italy-B had arisen between March and July 2017 in the central part of Lombardy and had spread westwards, circulating in the western part of Lombardy, Emilia Romagna, and Piedmont regions. This study was instrumental to reconstruct the virus dissemination routes and indicated that wild and domestic birds from Lombardy most likely represented the key source for the re-emergence and spread of the HPAI virus during the second and the third epidemic waves. This key spatial information will help to define appropriate disease control strategies.

Genetic diversity and re-classification of coffee (Coffea canephora Pierre ex A. Froehner) from South Western Nigeria through genotyping-by-sequencing-single nucleotide polymorphism analysis

Coffea canephora is an important economic crop in Nigeria, however, little is known about the diversity inherent within, and the genetic relationship among coffee grown and conserved in the country. We examined the genetic diversity and relatedness among 48 Coffea genotypes which included: (a) C. arabica, C. abeokutae, C. liberica, and C. stenophylla, (b) 14 C. canephora accessions conserved in the germplasm of Cocoa Research Institute of Nigeria (CRIN), and (c) 30 farmer-cultivated genotypes collected from South-Western Nigeria. By analyzing 433048 single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing we discovered that previous characterizations of C. canephora based on morphological data were inconclusive. Here, we established the correct number of C. canephora varieties present in the CRIN genebank which was four and not six as previously described based on morphological characters. We found three distinct diversity structures within the C. canephora genepool that were dominated by a single genetic group determined from passport descriptors to most likely be of Congolese (Democratic Republic of Congo) origin. High uniformity was also found among the farmer-cultivated accessions with 99% of them representing C. canephora var. Niaouli as their ancestral background. The analysis showed that the genetic base of coffee germplasm in Nigeria is narrow compared to the large genetic diversity of C. canephora. Therefore, broadening this genetic base through future acquisition and hybridization is imperative. However, the relatively high genetic differentiation (FST estimate = 0.3037) identified between Java Robusta and Niaouli will be used as a starting point for our breeding program.

Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast.

BackgroundThe mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil.MethodsNine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N.ResultsLoci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of FST (= 0.019; P < 0.001). FST and Jost’s D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs (P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition (P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation (FCT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation.DiscussionThe high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus. Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs.

Genetic Pattern and Demographic History of Salminus brasiliensis: Population Expansion in the Pantanal Region during the Pleistocene.

Pleistocene climate changes were major historical events that impacted South American biodiversity. Although the effects of such changes are well-documented for several biomes, it is poorly known how these climate shifts affected the biodiversity of the Pantanal floodplain. Fish are one of the most diverse groups in the Pantanal floodplains and can be taken as a suitable biological model for reconstructing paleoenvironmental scenarios. To identify the effects of Pleistocene climate changes on Pantanal’s ichthyofauna, we used genetic data from multiple populations of a top-predator long-distance migratory fish, Salminus brasiliensis. We specifically investigated whether Pleistocene climate changes affected the demography of this species. If this was the case, we expected to find changes in population size over time. Thus, we assessed the genetic diversity of S. brasiliensis to trace the demographic history of nine populations from the Upper Paraguay basin, which includes the Pantanal floodplain, that form a single genetic group, employing approximate Bayesian computation (ABC) to test five scenarios: constant population, old expansion, old decline, old bottleneck following by recent expansion, and old expansion following by recent decline. Based on two mitochondrial DNA markers, our inferences from ABC analysis, the results of Bayesian skyline plot, the implications of star-like networks, and the patterns of genetic diversity (high haplotype diversity and low-to-moderate nucleotide diversity) indicated a sudden population expansion. ABC allowed us to make strong quantitative inferences about the demographic history of S. brasiliensis. We estimated a small ancestral population size that underwent a drastic fivefold expansion, probably associated with the colonization of newly formed habitats. The estimated time of this expansion was consistent with a humid and warm phase as inferred by speleothem growth phases and travertine records during Pleistocene interglacial periods. The strong concordance between our genetic inferences and this historical data could represent the first genetic record of a humid and warm phase in the Pantanal in the period since the Last Interglacial to 40 ka.

RFLP-ANALYSIS OF BRADYRHIZOBIUM JAPONICUM NODULE BACTERIA, WIDESPREAD IN AGROCENOSIS OF UKRAINE

Aim. To investigate the genetic diversity of soybean nodule bacteria, widespread in agrocenoses of Ukraine. Methods. Nodule bacteria were isolated from soybean nodules grown in soil samples selected in different regions of Ukraine. The amplification of the intergenic region 16S-23S rRNA (ITS-region) was conducted with the use of primers FGPS1490-72 and FGPL132-38. For PCR-products restriction there were applied restriction endonucleases MspI, HaeIII and NdeII. Results. The diversity of Bradyrhizobium japonicum strains with different growthrates was investigated using PCR-RFLP method. According to analysis of 16S-23S rDNA with enzymes MspI, HaeIII and NdeII it was obtained that all the intensivegrowing strains had the same restriction profiles, so they were combined into a single genetic group. Based on ITS-region restriction the slow-growing strains were assigned into two genetic groups using MspI enzyme, three genetic groups using HaeIII and four genomogroups using NdeII enzyme. Сonclusions. High heterogeneity of B. japonicum strains allocated from soybean agrocenoses was found. They belong to different ITS-types according to the structure of intergenic region. Slow-growing strains used to be more heterogeneous, in comparison with more intensive-growth strains, which formed a homogeneous genomogroup.

Going, going, gone: evidence for loss of an endemic species pair of threespine sticklebacks (Gasterosteus aculeatus) with implications for protection under species-at-risk legislation

Genomic extinction occurs when the unique combination of genetic traits that characterize distinct phenotypes are eliminated by introgressive hybridization even if population size is greater than zero. Benthic and limnetic threespine sticklebacks (Gasterosteus aculeatus) constitute reproductively isolated undescribed biological species that have evolved independently in several lakes in southwestern British Columbia, Canada (known as “species pairs” in each lake). Here we investigated whether the two species that comprise the pair from Enos Lake, southeastern Vancouver Island, remain as two distinct gene pools. Multi-season samples (>1200 fish) obtained over two years from throughout the lake and assayed for variation in morphological traits characteristic of the two species (i.e., body depth, dorsal spine count, gill raker counts) and at 12 microsatellite DNA loci consistently indicated the existence of only a single group of sticklebacks. There was no consistent evidence of two groups in any morphological trait, and mean gill raker counts were consistently intermediate (20–21) to those of known benthics (~18) and limnetics (~24) which together comprised strikingly bimodal distributions in historical samples. Genetic analyses employing model-based clustering also consistently indicated the presence of only a single genetic group of sticklebacks. Compared to historical samples and to benthics and limnetics from other lakes, no Enos Lake fish could be identified confidently as a pure benthic or limnetic. Our results provide the strongest evidence yet that the Enos Lake sticklebacks now consist of a single morphological and genetic population of sticklebacks, that the unique combination of genetic and morphological traits that characterized benthic and limnetic sticklebacks no longer exist, and that their current status under Canada’s Species-at Risk Act as Endangered should be re-evaluated.

High genetic diversity and differentiation in three red tilapia stocks revealed by microsatellite DNA marker analysis

Red tilapia is thought to be the result of mutant-colored female Mozambique tilapias mating with male Nile, blue, or Zanzibar tilapias and cultured widely in Asia and central and South America. However, there is limited information about its genetic diversity and stock structure. In this study, we investigated the genetic variability of red tilapia stocks to provide fundamental knowledge for genetic improvement by molecular-marker-assisted selective breeding programs. Individuals (n = 180) from three stocks (Chinese Taiwan, Israel, and Malaysia) of red tilapia were genotyped based on 14 microsatellite markers. The results showed that all microsatellite loci were detected with high levels of polymorphism, with a mean number of 14.87 ± 3.85 alleles per locus in all stocks. Taiwan and Israel stocks showed higher heterozygosity than did the Malaysia stock. The F-statistic analysis showed that there was no significant genetic differentiation between the Taiwan and Israel stocks (P > 0.05), whereas there was highly significant genetic divergence in the other pairwise stocks (P < 0.01), suggesting that Taiwan and Israel stocks could be regarded as a single genetic group distinct from Malaysia stock. This result was in accordance with the UPGMA dendrogram based on Nei’s genetic distances of three stocks. The analysis of molecular variances (AMOVAs) revealed highly significant genetic variation among three stocks (P < 0.01) and accounted for 8.68% of the total variance. The results reported above were confirmed by Bayesian analysis in genetic structure simulation, which indicated a distinct genetic difference between Taiwan and Israel stocks compared with Malaysia stock.

Microsatellite based genetic diversity and mitochondrial DNA D-Loop variation in economically important goat breeds of Pakistan

The present study was undertaken to analyze the genetic diversity of five economically important goat breeds of Pakistan, Beetal, Kaghani, Teddy, Nachi and Pahari. Fifteen microsatellite loci recommended by ISAG/FAO guidelines were investigated for measures of genetic variability, differentiation and population structure. The genetic variability in terms of allelic diversity and heterozygosity were moderate. The estimated inbreeding coefficient was low in all the investigated goat breeds and not significant. Overall, the populations were less diverse than Eurasian goat breeds, but did not exhibit signs of loss of diversity. Analysis of molecular variance (AMOVA) showed breed differences accounted for 5.42% of total genetic variation indicating low to moderate genetic differentiation among the investigated goat breeds. The genetic structure analysis revealed Teddy, Pahari, and Nachi as distinct breeds, while Beetal and Kaghani form a single genetic group distinct from the other three goats. The mitochondrial DNA control region sequences showed a total of 60 distinct haplotypes belonging to two major maternal lineages A and B1 with a frequency of 76.9% and 23.1% respectively. Comparison of mtDNA sequences from Pakistani, Indian and Iranian goats indicated distinct evolutionary history for Teddy, Beetal, Nachi and Pahari goats different from that of Indian and Iranian goats.