Unrelated Males Research Articles

Haplotype diversity of 17 Y-STR in the Iranian population

The current study aimed to evaluate Y chromosome haplotypes obtained from 1353 unrelated Iranian males using the AmpFlSTRTM YfilerTM kit; 1353 out of the 1353 identified haplotypes were unique. The haplotype diversity (HD) and discriminating capacity (DC) values were 1.00000 and 0.997, respectively. Analysis of genetic distance was performed using molecular variance (AMOVA) and multidimensional scaling plots (MDS), revealing a statistically significant difference between the study population and previous data reported for other Iranian populations and other neighboring countries. The present findings are likely to be useful for forensic casework analyses and kinship investigations.

Haplotype of \(\textit{TEX15}\) single nucleotide variants associated with male infertility in 401 Vietnamese individuals

Spermatogenesis is a process of cell differentiation to produce fertilized sperm. Testis-expressed 15 (TEX15), an important gene in spermatogenesis, has been reported to be linked with male infertility in various populations. This study aimed to assess the association of single nucleotide polymorphism (SNP) TEX15 rs323347 with male infertile individuals in a Vietnamese cohort and further analyze the haplotypes of TEX15 rs323346 and TEX15 rs323347. A total of 401 unrelated males, including 202 male infertility patients and 199 healthy controls were genotyped for TEX15 rs323347 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Using statistical methods, the results showed that the allele frequencies of TEX15 rs323347 were in agreement with Hardy-Weinberg equilibrium (HWE) (p-value > 0.05), but its genotype frequencies were not significantly different between male infertility patient and control groups (p-values > 0.05). However, the CA haplotype of the two variants (rs323346 and rs323347) increased the risk of male infertility (p = 0.046, OR = 2.547, 95% CI = 0.982–6.602). Thus, this study would enrich the knowledge of the impact of genetic factors on male infertility in the Vietnamese population.

Revealing Y-STR Diversity of Koli Populations (Gujarat) by Studying 23 Y-STR Loci

Genetic analysis of Y-STR loci is pivotal for forensic libraries and genetic analysis. The Koli population in Gujarat, India, however, lacks such genetic characterization. This study aims to develop an allele frequency database for 23 Y-STR loci in the Koli population, examining forensic parameters and assessing genetic connections with neighboring tribes. A total of 153 unrelated Koli males were genotyped using the PowerPlex®Y23 multiplex commercial kit. We identified 117 distinct haplotypes. The Haplotype Diversity (HD) and Discrimination Capacity (DC) for the 23 Y-STR loci were 0.993 and 0.8034, respectively. DYS385b locus exhibited the highest allele variability (10 alleles), whereas DYS391, DYS389I, and DYS437 showed the least (4 alleles each). The highest Polymorphic Information Content (PIC) was observed in DYS385b (0.775), with the lowest in DYS391 (0.386). The dominant haplogroup R1a accounted for 45% of the population. Comparative analysis with other Indian populations from YHRD revealed two distinct clusters, placing the Koli population in cluster 2, indicating significant genetic similarity within this group. This inaugural study of Y-STRs in the Koli population demonstrates the utility of the Y23 kit in male identification, highlighted by substantial haplotype diversity and discrimination capacity.

Male-philopatric nonhuman primates and their potential role in understanding the evolution of human sociality.

In most primate species, males transfer out of their natal groups, resulting in groups of unrelated males. However, in a few species, including humans, males remain in their groups and form life-long associations with each other. This pattern of male philopatry is linked with cooperative male behaviors, including border patrols and predator defense. Because females in male-philopatric species form weaker kin networks with each other than in female-philopatric species, they are expected to evolve counter-strategies to male sexual coercion that are relatively independent of support from other females. Studies of male-philopatric nonhuman primates can provide insight into the evolutionary basis of prosocial behaviors, cooperation, and group action in humans and offer comparative models for understanding the sociality of other hominin species. This review will discuss patterns of dispersal and philopatry across primates, explore the resulting male and female behaviors, and argue that male-philopatric nonhuman primate species offer insight into the social and sexual dynamics of hominins throughout evolution.

Kin affiliation, socio-sexual and mating preference in the female Microtus ochrogaster in a multiple socio-sexual preference test

IntroductionThe prairie vole (Microtus ochrogaster) is a socially monogamous species that, after cohabitation with mating, forms an enduring pair bond. It has been suggested that female prairie voles avoid mating with fathers and siblings to prevent inbreeding depression. However, controlled laboratory tests of preferences involving males with varying degree of relatedness have not been conducted.MethodsTo address this, we employed a multiple socio-sexual preference arena consisting of four adjacent cylinders arranged in a closed circle. In each cylinder, we placed a male of varying relatedness to the experimental female (i.e., father, sibling, first-degree cousin, and unrelated males) and registered their behavior for five hours. Male socio-sexual preference was determined by the proportion of time spent in each male's chamber, which can be driven by affiliative preferences for the father and sibling and sexual attraction for the cousin and unrelated males. Mating preference was analyzed as the frequency of mating with each male. We hypothesized that receptive females would show sexual attraction and mating preferences for the unrelated males and cousins and affiliative preferences for the fathers and siblings.ResultsOur analyses showed that females spent more time with first-degree cousins and mated more often with them compared to unrelated males, siblings, or fathers. However, complete inbreeding avoidance was not observed, and some females mated with siblings, fathers, or both.DiscussionAlthough our results did not support the hypothesis, they are consistent with other studies that have argued that mating with first-degree cousins optimizes the costs and benefits associated with inbreeding and outbreeding.

Developmental validation of a novel 8-dye fluorescent typing system with 59 Y-STRs and 3 Y-indels for forensic applications.

An 8-dye fluorescence-labeling forensic Y-chromosomal short tandem repeats (Y-STRs) kit, the 62-plex Y-STR multiplex amplification system, was developed and optimized. The system was validated by testing PCR conditions, stutter ratios (SR) and peak height ratios, sensitivity, mixture samples, precision and accuracy, species-specificity, and inhibition studies according to the Scientific Working Group on DNA Analysis Methods guidelines. PCR-based studies showed that the recommended PCR conditions were optimized for this kit. In the sensitivity study, a full profile was obtained from template DNA with a quantity of u125pg. Consistent profiles were obtained from three different laboratories. The SRs in all loci were less than 15%, and nice balance and suitable average peak height were shown. No peaks were detected in the profiles of common animal species and microorganisms. In the male-male mixture studies, all loci were observed at a ratio of 1:8, and in the male-female mixture study, all alleles could be profiled at a ratio of 1:500 if the male DNA inputs were ≥0.5ng/µL. An inhibitor study demonstrated that the kit had varying degrees of resistance to the presence of common inhibitors. Population study demonstrated the 62-plex Y-STR Kit improved the power of discrimination in unrelated Chinese Han males (n=192). When haplotype diversity was 1, the probability of discrimination power of the 62-plex Y-STR Kit was 0.9948, which is suitable for forensic investigations. The results show that the developed 8-dye fluorescence labeling 62 loci system is sensitive, robust, convenient, and highly informative for forensic applications.

Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system

BackgroundMassively Parallel Sequencing (MPS) allowed an increased number of information to be retrieved from short tandem repeat (STR) analysis, expanding them not only to the size, as already performed in Capillary Electrophoresis (CE), but also to the sequence. MPS requires constant development and validation of the analytical parameters to ensure that the genotyping results of STRs correspond to those obtained by CE. Given the increased frequency of usage of Y-STRs as supplementary markers to the autosomal STRs analysis, it is urgent to validate the concordance of the typing results between CE and MPS analyses.Methods and resultsDNA extracted from 125 saliva samples of unrelated males was genotyped using Yfiler™ Plus PCR Amplification Kit and ForenSeq™ DNA Signature Prep Kit, which were analyzed by SeqStudio™ Genetic Analyzer for HID and MiSeq™ FGx Forensic Genomics System, respectively. For each shared Y-STR, allele designation, number of length- and sequence-based alleles per locus, stutter percentage, and the intra-locus balance of multicopy Y-STRs were screened.ConclusionsAlthough the number of forensic genetics laboratories that are applying the MPS technique in routine analysis is small and does not allow a global assessment of MPS limitations, this comparative study highlights the ability of MPS to produce reliable profiles despite the generation of large amounts of raw data.

Genetic analysis of 42 Y-STR loci in Han and Manchu populations from the three northeastern provinces in China

BackgroundY-STR polymorphisms are useful in tracing genealogy and understanding human origins and migration history. This study aimed to fill a knowledge gap in the genetic diversity, structure, and haplogroup distribution of the Han and Manchu populations from the three northeastern provinces in China (Liaoning, Jilin, and Heilongjiang).MethodsA total of 1,048 blood samples were collected from unrelated males residing in Dalian. Genotyping was performed using the AGCU Y37 + 5 Amplification Kit, and the genotype data were analyzed to determine allele and haplotype frequencies, genetic and haplotype diversity, discrimination capacity, and haplotype match probability. Population pairwise genetic distances (Fst) were calculated to compare the genetic relationships among Han and Manchu populations from Northeast China and other 23 populations using 27 Yfiler Plus loci set. Multi-dimensional scaling and phylogenetic analysis were employed to visualize the genetic relationships among the 27 populations. Moreover, haplogroups were predicted based on 27 Yfiler Plus loci set.ResultsThe Han populations from Northeast China exhibited genetic affinities with both Han populations from the Central Plain and the Sichuan Qiang population, despite considerable geographical distances. Conversely, the Manchu population displayed a relatively large genetic distance from other populations. The haplogroup analysis revealed the prevalence of haplogroups E1b1b, O1b, O2, and Q in the studied populations, with variations observed among different ethnic groups.ConclusionThe study contributes to our understanding of genetic diversity and history of the Han and Manchu populations in Northeast China, the genetic relationships between populations, and the intricate processes of migration, intermarriage, and cultural integration that have shaped the region’s genetic landscape.

The Qatari population's genetic structure and gene flow as revealed by the Y chromosome.

The Y-chromosome has been widely used in forensic genetic applications and human population genetic studies due to its uniparental origins. A large database on the Qatari population was created for comparison with other databases from the Arabian Peninsula, the Middle East, and Africa. We provide a study of 23 Y-STR loci included in PowerPlex Y23 (Promega, USA) that were genotyped to produce haplotypes in 379 unrelated males from Qatar, a country at the crossroads of migration patterns. Overall, the most polymorphic locus provided by the Promega kit was DYS458, with a genetic diversity value of 0.85 and a haplotype diversity of 0.998924. Athey's Haplogroup Predictor tool was used to predict haplogroups from Y-STR haplotypes in the Qatari population. In a median-joining network, the haplogroup J1 predominance (49%) in Qatar generated a star-like expansion cluster. The graph of population Q-matrix was developed using Y-STR data from 38 Middle Eastern and 97 African populations (11,305 individuals), and it demonstrated a stronger sub-grouping of countries within each ethnic group and showed the effect of Arabs on the indigenous Berbers of North Africa. The estimated migration rate between the Qatari and other Arabian populations was inferred using Bayesian coalescence theory in the Migrate-n program. According to the Gene Flow study, the main migration route was from Yemen to Kuwait through Qatar. Our research, using the PowerPlex Y23 database, shows the importance of gene diversity, as well as regional and social structuring, in determining the utility of demographic and forensic databases.

Primary azoospermia factor C duplication associated with spermatogenic impariment: a case-control study based on Y-chromosome haplogrouping in a Han Chinese population.

Azoospermia factor C (AZFc) in the male-specific region of Y-chromosome (MSY) presents wide structure variation mainly due to frequent non-allele homologous recombination, leading to significant copy number variation of the AZFc-linked coding sequences involving in spermatogenesis. A large number of studies had been conducted to investigate the association between AZFc deletions and male infertility in certain Y chromosome genetic backgrounds, however, the influence ofprimary AZFc duplication on spermatogenesis remained controversial and the cause of the discrepant outcomes is unknown. In the present study, a total of 1,102 unrelated Han Chinese males without any detectable AZF deletions were recruited from 2014 to 2019, including 411 controls with normozoospermia and 691 patients with idiopathic spermatogenic failure. Using multiple paralog ratio tests (PRTs), the structure duplications were classified by the copy number of the AZFc-linked amplicons and genes. The Y-chromosome haplogroup (Y-hg) was categorized by genetyping of MSY-linked polymorphism loci. The association of primary AZFc duplication with spermatogenic phenotype was investigated in males with the same Y-hg. Within Y-hg O3* group, the frequency of the gr/gr duplication in patients is significantly higher than that of controls (P=1.29×10-3 , odds ratio (OR) 7.64, 95% confidence interval (CI) 1.79-32.57). Moreover, Y-hg O3* males with the gr/gr duplication presented a significantly lower sperm production compared with non-AZFc duplicated ones (sperm concentration: P=1.46×10-3 ; total sperm count: P=1.82 ×10-3 ). The b2/b3 duplication were identified clustered in Y-hg Cα2*, and the significant difference in the distribution was not observed between patients with spermatogenic failure and controls. The results suggest that, in the Han Chinese population, the gr/gr duplication is a predisposinggenetic factor for spermatogenic impairment in males harboring Y-hg O3* . Meanwhile, the b2/b3 duplication may be fixed ona yet-unidentified subbranch of Y-hg Cα2* without significantly deleterious effect on spermatogenesis. Our findings provide evidence that the difference in the Y-hg composition may cause the discrepancy on the association of AZFc duplication with spermatogenic failure among the studied populations.

P-058 Defects in phospholipase C zeta cause polyspermy and low fertilization after conventional IVF: not just ICSI failure

Abstract Study question How does sperm phospholipase C zeta (PLCζ) affect fertilization in conventional in vitro fertilization (cIVF)? Summary answer Absence of PLCζ causes polyspermy, and a decline in the proportion of sperm expressing PLCζ is correlated with a low fertilization rate (FR) after cIVF. What is known already PLCζ is a key sperm-borne factor that triggers Ca2+ oscillations and the subsequent oocyte activation following gamete fusion. Mutations in PLCZ1, the gene encoding PLCζ, cause male infertility and intra-cytoplasmic sperm injection (ICSI) fertilization failure; and PLCζ expression and localization patterns are significantly correlated with ICSI FR. However, few studies have been published on the relationship between PLCζ and cIVF, an insemination procedure involving several key events that are bypassed in ICSI, e.g., sperm-zona binding and penetration, as well as polyspermy blocking. It is possible that sperm PLCζ may affect fertilization in a different manner from that in ICSI. Study design, size, duration Sixty couples who underwent cIVF treatments were recruited from the Reproductive and Genetic Hospital of CITIC-Xiangya between February 2019 and January 2022. Participants/materials, setting, methods We performed whole-exome sequencing in two unrelated males who exhibited infertility and polyspermy in cIVF. Immunofluorescence staining and oocyte-activation testing were employed to evaluate the effects of the candidate variants on PLCζ protein. Subsequent PLCζ analysis was performed in additional 58 males who underwent cIVF. The Pearson correlation coefficient was performed to evaluate the relationships between PLCζ and FRs. The receiver operating characteristic curve and Youden’s index analysis were used to indicate the cutoff value. Main results and the role of chance We identified one previously reported and two novel PLCZ1 variants in two males that were associated with male infertility and polyspermy characterized by excessive sperm–zona binding and a delay in pronuclear (PN) formation. In vitro functional analyses revealed that virtually all sperm from patients lacked functional PLCζ and were thus unable to evoke the physiologic pattern of Ca2+ oscillations. ICSI with an artificial oocyte-activation treatment successfully rescued the polyspermic phenotype and resulted in a live birth. Subsequent PLCζ analysis were performed in additional 58 males, who were allocated to three groups according to fertilization outcomes: a multiple pronuclear (MPN) group (no. of PN ≥ 3, MPN rate ≥ 50%, n = 9) and low fertilization (LF, total FR ≤ 30%, n = 18) and normal fertilization groups (NF, 2PN ≥ 50%, 1PN + MPN < 30%, n = 31). We found that the proportion of sperm that expressed PLCζ was positively correlated with both 2PN rate (P = 0.0005) and total FR (P = 0.0008) after cIVF, and that the optimal cutoff value below which males were likely to experience low FR (total FR ≤ 30%) after cIVF was 56.7% (area under the ROC curve, 0.705; P = 0.0176). Limitations, reasons for caution Precise mechanisms that underly the roles of PLCζ in cIVF outcomes are still uncovered. Follow-up studies with larger numbers of patients are required to validate the sensitivity, specificity, and accuracy of PLCζ as a diagnostic biomarker in cIVF outcomes. Wider implications of the findings Our study identified PLCZ1 as a novel causative gene of polyspermy in humans,highlighting the potential value of PLCζ as a fertility marker for cIVF outcomes. Trial registration number nor applicable

The evolution of early hominin food production and sharing

How did humans evolve from individualistic to collective foraging with sex differences in production and widespread sharing of plant and animal foods? While current evolutionary scenarios focus on meat, cooking, or grandparental subsidies, considerations of the economics of foraging for extracted plant foods (e.g., roots, tubers), inferred to be important for early hominins (∼6 to 2.5 mya), suggest that early hominins shared such foods with offspring and others. Here, we present a conceptual and mathematical model of early hominin food production and sharing, prior to the emergence of frequent hunting, cooking, and increased lifespan. We hypothesize that extracted plant foods were vulnerable to theft, and that male mate guarding protected females from food theft. We identify conditions favoring extractive foraging and food sharing across mating systems (i.e., monogamy, polygyny, promiscuity), and we assess which system maximizes female fitness with changes in the profitability of extractive foraging. Females extract foods and share them with males only when: i) extracting rather than collecting plant foods pays off energetically; and ii) males guard females. Males extract foods when they are sufficiently high in value, but share with females only under promiscuous mating and/or no mate guarding. These results suggest that if early hominins had mating systems with pair-bonds (monogamous or polygynous), then food sharing by adult females with unrelated adult males occurred before hunting, cooking, and extensive grandparenting. Such cooperation may have enabled early hominins to expand into more open, seasonal habitats, and provided a foundation for the subsequent evolution of human life histories.

Drivers and consequences of female reproductive competition in an egalitarian, sexually monomorphic primate

Even after the 150th anniversary of sexual selection theory, the drivers and mechanisms of female sexual selection remain poorly studied. To understand demographic circumstances favoring female-female competition, trade-offs with kin selection and interactions with male reproductive strategies, we investigated female evictions in redfronted lemurs (Eulemur rufifrons). Based on 24 years of demographic data of known individuals, we show that female redfronted lemurs target close female kin for forcible, permanent, and presumably lethal eviction, even though groups contain multiple unrelated males whose voluntary emigration actually mitigated the probability of future female evictions. Female eviction and male emigration were predicted by group size, but male emigration was primarily driven by a proportional increase of male rivals. Female evictions were more likely than male emigrations when there were more juvenile females in a group, but the identity of evicted females was not predicted by any intrinsic traits. While birth rates were reduced by the number of juvenile females, they were higher when there were more adult females in a group and in years with more rainfall. Early infant survival was reduced with increasing numbers of juvenile females, but variation in female lifetime reproductive success was not related to any of the predictors examined here. Thus, there seems to be a limit on female group size in this lemur species. More generally, our study demonstrates a balanced interplay between female reproductive competition, competition over group membership between both sexes, and kin selection, contributing new insights into the causes and consequences of female competition in animal societies.Significance statementThe evolutionary causes of female competition in vertebrate societies remain poorly known. Evictions represent an extreme form of female competition because even close kin are evicted when same-sized unrelated males are theoretically also available as victims. We studied drivers and consequences of evictions in redfronted lemurs (Eulemur rufifrons) using 24 years of demographic data from multiple groups. We show that while voluntary male emigration mitigates the probability of future female evictions, females nonetheless appear to accept the fitness costs of evicting female kin. While group size seems to be the main driver of departures by either sex, the number of juvenile females present in groups is the key variable triggering eviction events as well as physiological responses that could be interpreted as female reproductive restraint. Our study therefore revealed that competition does trump cooperation under some circumstances in the intricate interplay between sexual selection and kin selection on females.

Y-STR data of the Yfiler Plus panel in population of north-eastern Poland.

The use of new high-resolution and forensic identification capabilities for population studies offered by new multiplex methods (such as Yfiler Plus) is crucial in forensic genetics cases. The development of haplotype frequency databases is essential to take full advantage of the new Y chromosome determination capabilities. Development of the haplotype database of the Yfiler Plus kit for a population-based sample of 534 males from northeastern Poland and calculation of suitability parameters for forensic genetics studies. The study was conducted on a population sample of 534 unrelated males from the area of northeastern Poland using the Yfiler Plus panel of 27 markers located on the Y chromosome. Four haplotypes appeared twice. The Discrimination Capacity (DC) of the entire set was 0.9925. The highest Gene Diversity (GD) value was calculated for DYS518 (0.86) belonging to the fast-mutation markers, while the lowest GD was calculated for DYS392 (0.42). The results indicate the need for further research and observation of changes, both in different regions of Poland and across Europe.

Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father–son pairs

Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic genetics, and accurate knowledge of mutation rates at Y-STR loci is essential in kinship analysis. The main aim of this study was to estimate Y-STR mutation rates in Korean males. To obtain locus-specific mutations and haplotypes at 23 Y-STRs, we analyzed samples from 620 Korean father–son pairs. In addition, we also analyzed 476 unrelated individuals using the PowerPlex® Y23 System, with the aim of augmenting the available data for the Korean population. The PowerPlex® Y23 system facilitates analysis of the 23 Y-STR loci (DYS576, DYS570, DYS458, DYS635, DYS389 II, DYS549, DYS385, DYS481, DYS439, DYS456, DYS389 I, DYS19, DYS393, DYS391, DYS533, DYS437, DYS390, Y GATA H4, DYS448, DYS438, DYS392, and DYS643). Locus-specific mutation rate estimates varied from 0.00 to 8.06 × 10−3 per generation, with an average mutation rate of 2.17 × 10−3 (95% CI, 1.5–3.1 × 10−3). To obtain comprehensive genetic values for the Korean population, we combined data obtained in this study with previously reported values, thereby enabling us to estimate the locus-specific mutation rates regarding 22,711 allele transmissions. By combining these data, we obtained an overall average mutation rate of 2.91 × 10−3 (95% CI, 2.3–3.7 × 10−3). In addition, among the 476 unrelated Korean males, we detected 467 different haplotypes, with an overall haplotype diversity value of 0.9999. By extracting haplotypes of Y-STRs described in previous literature on 23 Y-STR reported in Korea, we obtained gene diversities for 1133 Korean individuals. We believe that the values and characteristics of the 23 Y-STRs analyzed in this study will contribute to establishing criteria for forensic genetic interpretation, including kinship analysis.

Genetic investigation of 124 SNPs in a Myanmar population using the Precision ID Identity Panel and the Illumina MiSeq

Single nucleotide polymorphisms (SNPs) have become popular in forensic genetics as an alternative to short tandem repeats (STRs). The Precision ID Identity Panel (Thermo Fisher Scientific), consisting of 90 autosomal SNPs and 34 Y-chromosomal SNPs, enabled human identification studies on global populations through next-generation sequencing (NGS). However, most previous studies on the panel have used the Ion Torrent platform, and there are few reports on the Southeast Asian population. Here, a total of 96 unrelated males from Myanmar (Yangon) were analyzed with the Precision ID Identity Panel on a MiSeq (Illumina) using an in-house TruSeq compatible universal adapter and a custom variant caller, Visual SNP. The sequencing performance evaluated by locus balance and heterozygote balance was comparable to that of the Ion Torrent platform. For 90 autosomal SNPs, the combined match probability (CMP) was 6.994 × 10−34, lower than that of 22 PowerPlex Fusion autosomal STRs (3.130 × 10−26). For 34 Y-SNPs, 14 Y-haplogroups (mostly O2 and O1b) were observed. We found 51 cryptic variations (42 haplotypes) around target SNPs, of which haplotypes corresponding to 33 autosomal SNPs decreased CMP. Interpopulation analysis revealed that the Myanmar population is genetically closer to the East and Southeast Asian populations. In conclusion, the Precision ID Identity Panel can be successfully analyzed on the Illumina MiSeq and provides high discrimination power for human identification in the Myanmar population. This study broadened the accessibility of the NGS-based SNP panel by expanding the available NGS platforms and adopting a robust NGS data analysis tool.

Genetic Relationship Between Founders of a Threatened Freshwater Turtle in a Mexican Wildlife Management Unit. A Conservation Strategy

Management Units for Wildlife Conservation (UMAs according to its Spanish acronym), are used for the ex-situ reproduction of freshwater turtles. These areas, often administered by local communities, are dedicated to conservation and sustainable management. The critically endangered freshwater turtle Dermatemys mawii has been successfully reproduced in several UMAs; however, no genetic management plan has been developed to maintain offspring genetic variability. Therefore, this study aims to determine the kinship relationship and homozygosity through the loci index of founder individuals in three UMAs devoted to the reproduction of D. mawii for the establishment of breeding groups. We collected skin samples of D. mawii in 2017 from 117 founder individuals from three UMAs located in the state of Tabasco, southeast Mexico. Ten specific D. mawii microsatellite markers were used for genotyping the founder individuals. We estimated the pedigree relationship between founders and proposed the formation of three breeding groups to optimize the use of related and non-related individuals to meet UMA-specific objectives and evaluated the genetic diversity retention of the breeding groups. The breeding groups were integrated as follows: 1) conservation breeding group consisting of 16 unrelated females and 7 unrelated males that presented a lower level of homozygosity (< 0.4); 2) research breeding group consisting of 45 females and 16 males that were unrelated or presented a half-sibling relationship and with a medium level of homozygosity (<0.6); and 3) a sustainable breeding group comprising 29 females and 4 males that were not necessarily unrelated and with a high level of homozygosity (> 0.6). Genetic diversity retention (Ho, He) was highest for the conservation breeder group and research breeder group. UMAs can create 3 breeding groups with different objectives: 1) species conservation, 2) research, and 3) sustainable use of species. All breeding groups can retain genetic diversity. Our proposal can enrich conservation actions and sustainable use for D. mawii at both national and international levels, specifically within the Mesoamerican corridor.

Y-chromosomal Short Tandem Repeat Variation in Kurd, Assyrian, and Armenian populations in Iraq Kurdistan

Background: North central Middle Eastern countries Iran, Iraq, Turkey, and Syria all have persistent Kurdish regions. Over thousands of years, several ethnicities have immigrated, settled, or resided in the region, including Turks, Persians, Arabs, Kurds, Armenians, Assyrians, Chechens, and Azeris. Methods: Eleven Y-chromosome STRs were evaluated in a total of 90 unrelated males from the Kurds, Armenians, and Assyrians populations in the Kurdistan region of Iraq (DYS19, DYS390, DYS393, DYS426, DYS437, DYS439, DYS447, DYS460, DYS461, DYS481, and DYS576). Using a DNA extraction kit, total DNA was isolated from leukocytes. PCR products were run on 8% polyacrylamide gel with a 50bp ladder DNA marker to size the bands, and silver staining was used to identify the DNA bands. Power Marker V3.25 software was used to determine variety of genetic parameters, including total allele number, allele frequency, gene diversity, polymorphic information content (PIC), and phylogenetic tree was constructed by MEGA-X software. Results: The total number of alleles identified in the three populations was 380. The sizes of the alleles ranged from 87bp to 275bp.The most diverse loci were DYS447 and DYS576 (GD: 0.949), whereas DYS426 showed the least diversity (GD:0.896). The Phylogenetic tree divided the populations into two main clusters: The Kurdish and Armenian clades in one cluster and the Assyrian in another cluster. Few of dendrogram leaves from the three examined groups were admixed with each other. Conclusions: This study confirms the high-resolution Y-STR typing's ability to discriminate. We conclude that the genetic distance between Kurd and Armenians is less than the genetic distance between the Kurd and the Assyrians, meaning that the Armenians population are genetically closer to the Kurds population.

Polymorphism and Mutation Rate of 20 Rapidly Mutating Y-Chromosomal Short Tandem Repeats in Chinese Han Population of Sichuan Province

To explore the applicability of 20 rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) in Chinese Han population of Sichuan province. Two RM Y-STR multiple amplification systems (RM1, including DYF404S1, DYF399S1, DYS547, DYS526a/b, DYS626, DYF403S1a/b, and DYS612, and RM2, including DYS1003, DYS1007, DYR88, DYS712, DYS711, DYS724, and DYF1002, with 14 RM Y-STR loci in total) and Y41SE-V1.2 (including 6 RM Y-STR loci of DYS627, DYS576, DYF387S1, DYS518, DYS570, and DYS449, 30 ordinary Y-chromosomal short tandem repeats [Y-STR] loci, and 1 Indel locus) were used for the amplification and typing of 200 unrelated males and 260 father-son pairs. The polymorphisms and mutation rates of 20 RM Y-STRs and 30 ordinary Y-STRs in Chinese Han population of Sichuan province were investigated and compared. In the 200 unrelated males, the gene diversity (GD) of 20 RM Y-STR loci ranged from 0.7910 to 0.9975, and there were 200 haplotypes. Haplotype diversity (HD) was 1 and the discriminative capacity (DC) was 1. A total of 198 haplotypes were found in Y41se-v1.2 (the 30 Y-STRs), with 4 cases sharing two haplotypes, the haplotype diversity being 0.9999, and the discriminative capacity being 0.99. A total of 68 mutations were found at the 20 RM Y-STRs loci in the 260 father-son pairs, and there was slightly more increase than decrease of allele repeats (1.19∶1), with the mutation rate ranging from <3.85×10 -3 (95% C I: 0.00-1.41×10 -2) to 2.69×10 -2 (95% CI: 1.09×10 -2-5.47×10 -2), and the average mutation rate being 1.19×10 -2 (95% CI: 9.20×10 -3-1.51×10 -2). The 20 RM Y-STRs and the Y41SE-V1.2 (the 30 Y-STRs) could be used to distinguish 22.3% and 13.8% father-son pairs, respectively. The 20 RM Y-STRs have high gene and haplotype diversity and paternal lineage differentiation rate in Chinese Han population of Sichuan province, showing great potential for application in Chinese Han population of Sichuan province.

MED12 variants associated with X-linked recessive partial epilepsy without intellectual disability

ObjectivesThe MED12 gene encodes mediator complex subunit 12, which is a component of the mediator complex involved in the transcriptional regulation of nearly all RNA polymerase II-dependent genes. MED12 variants have previously been associated with developmental disorders with or without nonspecific intellectual disability. This study aims to explore the association between MED12 variants and epilepsy. Materials and methodsTrios-based whole-exome sequencing was performed in a cohort of 349 unrelated cases with partial (focal) epilepsy without acquired causes. The genotype-phenotype correlations of MED12 variants were analyzed. ResultsFive hemizygous missense MED12 variants, including c.958A>G/p.Ile320Val, c.1757G>A/p.Ser586Asn, c.2138C>T/p.Pro713Leu, c.3379T>C/p.Ser1127Pro, and c.4219A>C/p.Met1407Leu were identified in five unrelated males with partial epilepsy. All patients showed infrequent focal seizures and achieved seizure free without developmental abnormalities or intellectual disability. All the hemizygous variants were inherited from asymptomatic mothers (consistent with the X-linked recessive inheritance pattern) and were absent in the general population. The two variants with damaging hydrogen bonds were associated with early-onset seizures. Further genotype-phenotype analysis revealed that congenital anomaly disorder (Hardikar syndrome) was associated with (de novo) destructive variants in an X-linked dominant inheritance pattern, whereas epilepsy was associated with missense variants in an X-linked recessive inheritance pattern. Phenotypic features of intellectual disability appeared as the intermediate phenotype in terms of both genotype and inheritance. Epilepsy-related variants were located at the MED12-LCEWAV domain and the regions between MED12-LCEWAV and MED12-POL. ConclusionMED12 is a potentially causative gene for X-linked recessive partial epilepsy without developmental or intellectual abnormalities. The genotype-phenotype correlation of MED12 variants explains the phenotypic variations and can help the genetic diagnosis.