Shared Haplotypes Research Articles

Morphological Ontogeny, Ecology, and Biogeography of Fuscozetes fuscipes (Acari, Oribatida, Ceratozetidae).

The systematic status of Fuscozetes Sellnick, 1928, is not clear in the literature. Therefore, the morphological ontogeny of F. fuscipes (C.L. Koch, 1844), the type species of this genus, was investigated and compared with its congeners in this study, and a new diagnosis of Fuscozetes is given. The juveniles of F. fuscipes are light brown, with a brown prodorsum, sclerites, epimeres, and legs. In all juveniles, a humeral organ and a humeral macrosclerite are present. The gastronotum of the larva has 12 pairs of setae (h3 is present), whereas the nymphs have 15 pairs. In the larva, the gastronotal shield is weakly developed, and most gastronotal setae are short except for a slightly longer h2. Most of the gastronotal setae are inserted on the microsclerites except for h3, and several other macrosclerites and many microsclerites are present on the hysterosoma. In the nymphs, the gastronotal shield is well developed, with 10 pairs of setae (d-, l-, and h-series, and p1), and setae p2 and p3 are located on a large posteroventral macrosclerite. In all the instars, femora I and II are oval in cross-section, without a large ventral carina. Mitochondrial COI sequence data revealed a deep split between the Nearctic and Palearctic populations of F. fuscipes, and a less, but significant, divergence within each continent. These strong geographical barriers were contrasted with multiple cases of shared haplotypes over long distances in the Palearctic, indicating high migration rates in modern times.

Identification of a founder variant AAGAB c.370C>T, p.Arg124Ter in patients with punctate palmoplantar keratoderma in Southern Denmark.

Palmoplantar keratoderma (PPK) is a heterogeneous group of rare skin diseases characterized by hyperkeratosis on the palms or soles. The subtype isolated punctate PPK is caused by heterozygous variants in AAGAB. We investigated if the variant AAGAB c.370C>T, p.Arg124Ter in patients with punctate PPK in the Region of Southern Denmark represented a founder variant and estimated the age to the most recent common ancestor. We performed haplotype analysis on samples from 20 patients diagnosed with punctate PPK and the AAGAB c.370C>T, p.Arg124Ter variant. Using the Gamma Method, we calculated the years to the most recent common ancestor. We also explored the presence of the variant in other populations through literature and databases (HGMD, ClinVar, and gnomAD). Our analysis revealed a shared haplotype of 3.0 Mb, suggesting shared ancestry. The ancestral haplogroup was estimated to an age of 12.1 generations (CI: 4.9-20.3) equivalent to approximately 339 years (CI: 137-568). This study confirms that the frequently observed variant AAGAB c.370C>T, p.Arg124Ter in punctate PPK among patients in the Region of Southern Denmark is caused by a founder variant. We recommend testing for the variant as initial screening in our region and potentially for all Danish patients presenting with punctate PPK.

Genetic Structure of Gallus varius Based on Middle-Lower Section of Control Region mtDNA

Gallus varius, an indigenous bird species of Indonesia, demonstrates significant genetic diversity. The genetic diversity assessment in G. varius encompassed both mitochondrial DNA (mtDNA) and nuclear DNA, with the mtDNA analysis primarily centered on domain I of the control region. This study aimed to describe the genetic diversity and structure of G. varius inhabiting Java, Madura, Lombok and Sumbawa based on the middle-lower part of control region mtDNA. Genomic DNA was extracted from the calamus tip of feather, then the middle-lower part of control region was amplified and sequenced using two pairs of primers. In the examined control region, spanning from 944 to 1,008 bp, 13 bp of nucleotide variation was observed, with nucleotide diversity at 0.0021. Between G. varius samples and the reference (NC_007238.1), a total of 7 haplotypes were identified, 5 unique and 2 shared haplotypes, with haplotype diversity at 0.7692. The substantial diversity of haplotypes in this study and two previous study suggests that the genetic diversity of G. varius has remained stable over the past two decades. Additionally, genetic distance data indicate there is multiple G. varius subspecies, and the haplotype network accentuates signs of population differentiation.

Clinical, biochemical, and genetic spectrum of MADD in a South African cohort: an ICGNMD study

BackgroundMultiple acyl-CoA dehydrogenase deficiency (MADD) is an autosomal recessive disorder resulting from pathogenic variants in three distinct genes, with most of the variants occurring in the electron transfer flavoprotein-ubiquinone oxidoreductase gene (ETFDH). Recent evidence of potential founder variants for MADD in the South African (SA) population, initiated this extensive investigation. As part of the International Centre for Genomic Medicine in Neuromuscular Diseases study, we recruited a cohort of patients diagnosed with MADD from academic medical centres across SA over a three-year period. The aim was to extensively profile the clinical, biochemical, and genomic characteristics of MADD in this understudied population.MethodsClinical evaluations and whole exome sequencing were conducted on each patient. Metabolic profiling was performed before and after treatment, where possible. The recessive inheritance and phase of the variants were established via segregation analyses using Sanger sequencing. Lastly, the haplotype and allele frequencies were determined for the two main variants in the four largest SA populations.ResultsTwelve unrelated families (ten of White SA and two of mixed ethnicity) with clinically heterogeneous presentations in 14 affected individuals were observed, and five pathogenic ETFDH variants were identified. Based on disease severity and treatment response, three distinct groups emerged. The most severe and fatal presentations were associated with the homozygous c.[1067G > A];c.[1067G > A] and compound heterozygous c.[976G > C];c.[1067G > A] genotypes, causing MADD types I and I/II, respectively. These, along with three less severe compound heterozygous genotypes (c.[1067G > A];c.[1448C > T], c.[740G > T];c.[1448C > T], and c.[287dupA*];c.[1448C > T]), resulting in MADD types II/III, presented before the age of five years, depending on the time and maintenance of intervention. By contrast, the homozygous c.[1448C > T];c.[1448C > T] genotype, which causes MADD type III, presented later in life. Except for the type I, I/II and II cases, urinary metabolic markers for MADD improved/normalised following treatment with riboflavin and L-carnitine. Furthermore, genetic analyses of the most frequent variants (c.[1067G > A] and c.[1448C > T]) revealed a shared haplotype in the region of ETFDH, with SA population-specific allele frequencies of < 0.00067–0.00084%.ConclusionsThis study reveals the first extensive genotype–phenotype profile of a MADD patient cohort from the diverse and understudied SA population. The pathogenic variants and associated variable phenotypes were characterised, which will enable early screening, genetic counselling, and patient-specific treatment of MADD in this population.

Population structure and demographic history for year cohort dynamics of landlocked ayu Plecoglossus altivelis altivelis in dam reservoir of Japan.

Ayu Plecoglossus altivelis altivelis is a valuable osmeroid species for inland fishery in Japan. It is classified into two ecological forms of amphidromous migrating between rivers and sea and landlocked migrating between rivers and lakes or dam reservoirs. The number of dams and their reservoirs has remarkably increased in the twenty-first century under climate change, because of their respective roles in hydropower generation with negligible carbon emissions and in flood control. Dam reservoirs therefore become increasingly important as inland nursery grounds of ayu. In this study, we investigated the reproduction status of landlocked ayu migrating in the Haidzuka Dam reservoir and the Tabusa River in western Japan by molecular phylogenetic analysis based on population structure and demographic history for year cohort dynamics. A total of 849 individuals were collected monthly from October 2018 to September 2021 according to an annual life cycle of ayu. Nucleotide sequences of the partial mitochondrial DNA control region yielded 31 haplotypes, consisting of 4 shared haplotypes among the 2019, 2020 and 2021 cohorts and 27 unique haplotypes. The overall haplotype diversity and nucleotide diversity were calculated to be relatively low at 0.3503 ± 0.0206 and 0.0077 ± 0.0045, respectively, suggesting a founder event by dominant haplotypes. Star-shaped radiational haplotypes from dominant shared haplotypes on the median-joining network likely support a founder event. Although pairwise ФST values were determined to be very low among the year cohorts, only the 2019 cohort was found to have a significant difference from the 2020 and 2021 cohorts, for both of which Tajima's D values were also statistically significant. For the overall population, multimodal mismatch distribution and negative Tajima's D and Fu's Fs values in the neutrality test suggested population expansion or population subdivision. The native riverine population in the Tabusa River suffered habitat fragmentation and population bottleneck from dam construction, and therefore severe founder effect remained behind the artificially landlocked population with a low level of genetic diversity in the Haidzuka Dam reservoir.

Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs

BackgroundEurasian pigs have undergone lineage admixture throughout history. It has been confirmed that the genes of indigenous pig breeds in China have been introduced into Western commercial pigs, providing genetic materials for breeding Western pigs. Pigs in Taihu Lake region (TL), such as the Meishan pig and Erhualian pig, serve as typical representatives of indigenous pig breeds in China due to their high reproductive performances. These pigs have also been imported into European countries in 1970 and 1980 s. They have played a positive role in improving the reproductive performances in European commercial pigs such as French Large White pigs (FLW). However, it is currently unclear if the lineage of TL pigs have been introgressed into the Danish Large White pigs (DLW), which are also known for their high reproductive performances in European pigs. To systematically identify genomic regions in which TL pigs have introgressed into DLW pigs and their physiological functions, we collected the re-sequencing data from 304 Eurasian pigs, to identify shared haplotypes between DLW and TL pigs.ResultsThe findings revealed the presence of introgressed genomic regions from TL pigs in the genome of DLW pigs indeed. The genes annotated within these regions were found to be mainly enriched in neurodevelopmental pathways. Furthermore, we found that the 115 kb region located in SSC16 exhibited highly shared haplotypes between TL and DLW pigs. The major haplotype of TL pigs in this region could significantly improve reproductive performances in various pig populations. Around this genomic region, NDUFS4 gene was highly expressed and showed differential expression in multiple reproductive tissues between extremely high and low farrowing Erhualian pigs. This suggested that NDUFS4 gene could be an important candidate causal gene responsible for affecting the reproductive performances of DLW pigs.ConclusionsOur study has furthered our knowledge of the pattern of introgression from TL into DLW pigs and the potential effects on the fertility of DLW pigs.

The Genetic Diversity of White-Backed Planthoppers (Sogatella furcifera) between Myanmar and Yunnan Province of China.

In order to clarify the migration route and the source of white-backed planthopper (WBPH) (Sogatella furcifera) between Myanmar and Yunnan Province, China, we collected six populations throughout Myanmar and five populations around the border areas in Yunnan Province, China. A total of 790 base pairs in the mtDNA COI genes from 416 individuals were obtained. A total of 43 haplotypes were identified, among which 37 were unique haplotypes, and the remaining 6 were shared among different populations. Two common shared haplotypes (H_1 and H_2) had a widespread distribution in all populations and accounted for 88.8% of the total haplotype frequency, suggesting a high-level gene flow among the Myanmar and Yunnan populations. Bayesian skyline plot (BSP) analysis results indicated that the effective population size of WBPH expanded between about 10,000 and 7000 years ago, and S. furcifera might follow the post-LGM (Last Glacial Maximum) expansion pattern. Based on the total migrant (Nem) value, it can be deduced that north and northeast Myanmar were the primary migration sources for WBPH populations in the southwest and south Yunnan regions. This study aims to contribute to the sustainable regional management of this important rice pest and provide new insights into the genetic diversity of WBPH in Southeast Asia.

Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal

We here analyze data from the first year of an ongoing nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal. The analysis is based on 1097 samples collected at health facilities during passive malaria case detection in 2019; it provides a baseline for analyzing parasite genetic metrics as they vary over time and geographic space. The study’s goal was to identify genetic metrics that were informative about transmission intensity and other aspects of transmission dynamics, focusing on measures of genetic relatedness between parasites. We found the best genetic proxy for local malaria incidence to be the proportion of polygenomic infections (those with multiple genetically distinct parasites), although this relationship broke down at low incidence. The proportion of related parasites was less correlated with incidence while local genetic diversity was uninformative. The type of relatedness could discriminate local transmission patterns: two nearby areas had similarly high fractions of relatives, but one was dominated by clones and the other by outcrossed relatives. Throughout Senegal, 58% of related parasites belonged to a single network of relatives, within which parasites were enriched for shared haplotypes at known and suspected drug resistance loci and at one novel locus, reflective of ongoing selection pressure.

Integrative taxonomy and evolutionary history reveal cryptic diversity in Myotis riparius (Chiroptera: Vespertilionidae)

Abstract Myotis riparius is an insectivorous bat species widely distributed in the Neotropics with evident geographical variation in morphological traits. We conducted an integrative study using mitochondrial DNA, qualitative and quantitative morphology, and current and past species distribution models to investigate the variation, population structure, and distributional limits within M. riparius populations. Phylogenetic inferences indicated that M. riparius is monophyletic, and populations are divided into geographically structured clades that split during the middle Pleistocene. There is no shared haplotype between geographical populations and strong evidence of partial restriction in gene flow. Morphological and morphometric variations revealed subtle distinctions among different populations, but little correspondence with molecular analysis. The distribution models indicated that M. riparius is associated with forest environments, with discontinuity between populations from South American ecoregions. Past distribution modelling, however, indicated that M. riparius had a larger distribution range in the Last Glacial Maximum than currently. Results of modelling and genetic analyses indicated that M. riparius consisted of a large, widespread, and panmictic (meta)population until the middle Pleistocene, when environmental changes driven by climatic dynamics fragmented and isolated the populations. Myotis riparius is here considered a complex of at least four allopatric and parapatric cryptic evolutionary units.

Genetic and Haplotype Diversity of Manila Clam Ruditapes philippinarum in Different Regions of China Based on Three Molecular Markers.

China has the largest production yield of Manila clam Ruditapes philippinarum in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand the genetic and haplotype diversity of R. philippinarum, 14 clam populations sampled from different regions of China were analyzed by three molecular markers, including COI, 16SrRNA and ITS. Based on the results of the COI and ITS genes, the 14 populations showed a moderate to high level of genetic diversity, with an average haplotype diversity of 0.9242 and nucleotide diversity of 0.05248. AMOVA showed that there was significant genetic differentiation among all populations (mean FST of the total population was 0.4534). Pairwise FST analysis showed that genetic differentiation reached significant levels between Laizhou and other populations. Two Laizhou populations showed great divergence from other populations, forming an independent branch in the phylogenetic tree. The shared haplotypes Hap_2 and Hap_4 of COI appeared most frequently in most clam populations. In contrast, 16SrRNA analysis of the clam populations revealed the dominated haplotype Hap_2, accounting for 70% of the total number of individuals. The haplotype diversity of the Laizhou population (Laizhou shell-wide (KK) and Laizhou dock (LZMT)) was relatively higher than other populations, showing multiple unique haplotypes (e.g., Hap_40, Hap_41 and Hap_42). These findings of genetic and haplotype diversity of clam populations provide guiding information for genetic resource conservation and genetic improvement of the commercially important R. philippinarum.

Variable clinical expression of a Belgian TGFB3 founder variant suggests the presence of a genetic modifier.

Background: TGFB3 variants cause Loeys-Dietz syndrome type 5, a syndromic form of thoracic aortic aneurysm and dissection. The exact disease phenotype is hard to delineate because of few identified cases and highly variable clinical representation. Methodology: We provide the results of a haplotype analysis and a medical record review of clinical features of 27 individuals from 5 different families, originating from the Campine region in Flanders, carrying the NM_003239.5(TGFB3):c.787G>C p.(Asp263His) likely pathogenic variant, dbSNP:rs796051886, ClinVar:203492. The Asp263 residue is essential for integrin binding to the Arg-Gly-Asp (RGD) motif of the TGFβ3-cytokine. Results: The haplotype analysis revealed a shared haplotype of minimum 1.92Mb and maximum 4.14Mb, suggesting a common founder originating >400years ago. Variable clinical features included connective tissue manifestations, non-aneurysmal cardiovascular problems such as hypertrophic cardiomyopathy, bicuspid aortic valve, mitral valve disease, and septal defects. Remarkably, only in 4 out of the 27 variant-harboring individuals, significant aortic involvement was observed. In one family, a 31-year-old male presented with type A dissection. In another family, the male proband (65years) underwent a Bentall procedure because of bicuspid aortic valve insufficiency combined with sinus of Valsalva of 50mm, while an 80-year-old male relative had an aortic diameter of 43mm. In a third family, the father of the proband (75years) presented with ascending aortic aneurysm (44mm). Conclusion: The low penetrance (15%) of aortic aneurysm/dissection suggests that haploinsufficiency alone by the TGFB3 variant may not result in aneurysm development but that additional factors are required to provoke the aneurysm phenotype.

Contrasting results of multiple species delimitation approaches cause uncertainty in synecological studies: A case study on Sri Lankan chafers

Abstract Biodiversity patterns are the sum of multiple overlapping species distributions. Their analysis therefore requires proper species inference. DNA‐based species delimitation has become increasingly popular for such assessments, but their robustness is often problematic due to incongruence between multiple delimitation approaches. Here, we explored how contrasting results of different species’ delimitations translate into conclusions of synecological studies, exemplified by assemblages of phytophagous scarab beetles in Sri Lanka from different elevations and forest types. Particularly, we compared estimates based on complete assemblages and on cumulated species inventories inferred from individually analysed subclades. The patterns of assemblage similarity were analysed across different spatial scales with reference to morphospecies, molecular operational taxonomic units (MOTUs) and haplotypes. Method‐related ambiguity of species (MOTUs) estimates, which also included subclade inferences, severely affected the certainty of apparent biodiversity patterns at most spatial scales. Even more contrasting patterns resulted from individual clade‐wise analyses of faunal similarity or even from cumulated species inventories from individual clade‐wise species delimitation analysis. In this case study of tropical chafer beetles, haplotypes provided only very little explanatory information, since genetically highly diverse populations widely lacked shared haplotypes. Therefore, searching proper species boundaries should be the ultimate goal of biodiversity assessments to lend an enduring meaning to biodiversity research and its sustainable application. Our study underlines the need for awareness when synecological observations from different studies are integrated, which use different species delimitation methods for their biodiversity assessment, and its potential impact on conservation management.

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene.

To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima's D and Fu's Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima's D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.

Phenotypic variability of filamin C–related cardiomyopathy: Insights from a novel Dutch founder variant

Dilated cardiomyopathy (DCM) can be caused by truncating variants in the filamin C gene (FLNC). A new pathogenic FLNC variant, c.6864_6867dup, p.(Val2290Argfs*23), was recently identified in Dutch DCM patients. The report aimed to evaluate the phenotype of FLNC variant carriers and to determine whether this variant is a founder variant. Clinical and genetic data were retrospectively collected from variant carriers. Cardiovascular magnetic resonance (CMR) studies were reassessed. Haplotypes were reconstructed to determine a founder effect. The geographical distribution and age of the variant were determined. Thirty-three individuals (70% female) from nine families were identified. Sudden cardiac death was the first presentation in a carrier at 28 years of age. Median age at diagnosis was 41 years (range 19-67). The phenotype was heterogeneous. DCM with left ventricular (LV) dilation and reduced ejection fraction (<45%) was present in eleven individuals (33%), three (9%) of whom underwent heart transplantation. CMR showed late gadolinium enhancement (LGE) in 65% of the assessed individuals, primarily in a ring-like distribution. Non-sustained ventricular arrhythmias were detected in six (18%), and five (15%) individuals received an implantable cardioverter defibrillator. A shared haplotype spanning 2.1 Mb was found in all haplotyped individuals. The variant originated between 275-650 years ago. The pathogenic FLNC variant c.6864_6867dup, p.(Val2290Argfs*23) is a founder variant originating from the south of the Netherlands. Carriers are susceptible to developing heart failure and ventricular arrhythmias. The cardiac phenotype is characterized by ring-like LGE, even in individuals without significantly reduced LV function.

Population genetic structure of the bentfin devil ray (Mobula thurstoni) in the South Indonesia Sea with limited sample based on ND5 gene

Abstract. Wardana ED, Putra ING, Al Malik MD, Yusmalinda NLA, Ningsih EY, Pertiwi NPD, Salim MG, Kanedi MM, Putra MIH, Sembiring A. 2023. Population genetic structure of the bentfin devil ray (Mobula thurstoni) in the South Indonesia Sea with limited sample based on ND5 gene. Biodiversitas 24: 3743-3749. Bentfin devil ray (Mobula thurstoni) is one of five Mobula rays with a worldwide distribution. This species has high economic value and play an essential ecological role. However, due to their biological characteristics, such as low reproductive rates and late maturity, these species are highly vulnerable to overfishing and slow to recover from depletion. Genetic information, such as this species's population structure and genetic diversity is limited. This study aimed to determine the genetic variation and population structure of M. thurstoni in the South Indonesia Sea based on mitochondrial DNA from ND5 gene. Twenty-two samples of M. thurstoni were successfully collected from three locations Palabuhanratu (n=5), Muncar (n=13), and Savu Sea (n= 4). The haplotype diversity (Hd) ranged from 0.782 to 1.00 (mean=0.839), and Nucleotide diversity (?) ranged from 0.004 to 0.018 (mean=0.007). Then, no significant population differences (P-value &gt; 0.05) were observed between locations, indicating that M. thurstoni population in the South Indonesian Sea represents a single genetic population. Additionally, the haplotype distribution also indicated the presence of two shared haplotypes between locations. Consequently, co-management strategies for sustainable fishing and conservation must be implemented across these three locations to ensure the sustainability of this species in the nature habitat.

First Discovery of the North American Leaf-Mining Moth Chrysaster ostensackenella (Lepidoptera: Gracillariidae) in Russia: The Genetic Diversity of a Novel Pest in Invaded vs. Native Range.

Here, we report the first detection of the North American leaf-mining moth Chrysaster ostensackenella (Fitch, 1859) (Lepidoptera: Gracillariidae) on North American black locust Robinia pseudoacacia (Fabaceae) in Primorsky Krai (the Russian Far East) in July 2022. Overall, six moths were reared from the leaf mines and identified based on adult morphology (forewing pattern and male genitalia) and three of them were DNA barcoding. Description of the leaf mines that allowed us to distinguish the damage of Ch. ostensackenella from other gracillariids associated with R. pseudoacacia is provided. The phylogeographic analysis comparing the DNA barcodes from Russia with those from other invaded countries in Europe (Italy) and East Asia (South Korea and Japan) and from the native range (North America) was performed. Intraspecific genetic diversity reached 3.29%. Altogether, 10 haplotypes were revealed among 21 studied specimens in the Holarctic. The detection of one haplotype common for Japan and the USA (North Carolina) suggests that the invasion to East Asia could have happened from the USA directly, rather than through Europe. A shared haplotype defined for Japan and the Russian Far East points at a possible moth species' spread to Primorsky Krai from earlier invaded Hokkaido. Further distribution of Ch. ostensackenella in East Asia and Europe is expected, bearing in mind the wide planting of R. pseudoacacia in these continents. Furthermore, an accidental introduction of the moth to the Southern Hemisphere, where black locust was introduced, is not ruled out.

Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys

To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.

Spatial and temporal diversity of positive selection on shared haplotypes at the PSCA locus among worldwide human populations.

Selection on standing genetic variation is important for rapid local genetic adaptation when the environment changes. We report that, for the prostate stem cell antigen (PSCA) gene, different populations have different target haplotypes, even though haplotypes are shared among populations. The C-C-A haplotype, whereby the first C is located at rs2294008 of PSCA and is a low risk allele for gastric cancer, has become a target of positive selection in Asia. Conversely, the C-A-G haplotype carrying the same C allele has become a selection target mainly in Africa. However, Asian and African share both haplotypes, consistent with the haplotype divergence time (170 kya) prior to the out-of-Africa dispersal. The frequency of C-C-A/C-A-G is 0.344/0.278 in Asia and 0.209/0.416 in Africa. Two-dimensional site frequency spectrum analysis revealed that the extent of intra-allelic variability of the target haplotype is extremely small in each local population, suggesting that C-C-A or C-A-G is under ongoing hard sweeps in local populations. From the time to the most recent common ancestor (TMRCA) of selected haplotypes, the onset times of positive selection were recent (3-55 kya), concurrently with population subdivision from a common ancestor. Additionally, estimated selection coefficients from ABC analysis were up to ~3%, similar to those at other loci under recent positive selection. Phylogeny of local populations and TMRCA of selected haplotypes revealed that spatial and temporal switching of positive selection targets is a unique and novel feature of ongoing selection at PSCA. This switching may reflect the potential of rapid adaptability to distinct environments.

Genetic differences between western and eastern gray whales (Eschrichtius robustus)

Molecular data were used to examine the differentiation between the western and eastern gray whale (Eschrichtius robustus) populations. Control region sequences were generated from samples collected in the western Pacific (n = 45) and eastern Pacific (n = 120). There were 36 unique haplotypes identified. Ten haplotypes were represented in the western samples, and 33 in the eastern samples. Seven of these haplotypes were shared between populations, leaving three haplotypes that were only seen in the western samples and 26 only in the eastern. Although there were no fixed (diagnostic) differences between the western and eastern groups, they were significantly different in their haplotype frequency distributions and should be considered as separate populations. None of the 33 haplotypes found in the eastern samples had a frequency of over 11%, yielding an estimated haplotypic diversity of 0.95. This finding indicates that the reduction in abundance due to whaling may not have had a great effect on the haplotypic diversity of the eastern population, although the loss of rare haplotypes may still have occurred and would be difficult to detect. In contrast, the western group was dominated by two haplotypes, which represented over 77% of all individuals sampled, resulting in a substantially lower haplotypic diversity of 0.70. The lack of fixed differences between the two populations and frequency of shared haplotypes renders these data inappropriate for forensic applications at the population level.

Spinocerebellar Ataxia 36 is a Frequent Cause of Hereditary Ataxia in Eastern Spain.

Autosomal dominant spinocerebellar ataxia 36 (SCA36) is caused by hexanucleotide repeat expansion in the NOP56 gene. To assess frequency, clinical and genetic features of SCA36 in Eastern Spain. NOP56 expansion was tested in a cohort of undiagnosed cerebellar ataxia families (n = 84). Clinical characterization and haplotype studies were performed. SCA36 was identified in 37 individuals from 16 unrelated families. It represented 5.4% of hereditary ataxia patients. The majority were originally from the same region and displayed a shared haplotype. Mean age at onset was 52.5 years. Non-ataxic features included: hypoacusis (67.9%), pyramidal signs (46.4%), lingual fasciculations/atrophy (25%), dystonia (17.8%), and parkinsonism with evidence of dopaminergic denervation (10.7%). SCA36 is a frequent cause of hereditary ataxia in Eastern Spain, and is associated with a strong founder effect. SCA36 analysis should be considered prior to other studies, especially in AD presentations. Parkinsonism reported here broadens SCA36 clinical spectrum.