Paternal Lineages Research Articles

Phylogeographic analysis of Y-chromosomal haplogroup C2a-M48-F8472, a minor paternal lineage of Han populations with possible ancestry of Xiongnu

Background Y-chromosome haplogroup C2a-M48-F8472, a unique paternal line in the ancient Xiongnu population, is concentrated in the modern Han people. The most closely related lineage of this paternal lineage is mainly distributed in Tungusic-, Mongolic-, and Turkic-speaking populations. Aim To investigate the formation process of this unique distribution state. Subjects and methods In total, 36 sequences of haplogroup C2a-M48-F8472 were analysed to generate a revised phylogenetic tree with age estimation and to explore the geographic distribution pattern. Results The results suggested that northern China is likely the diffusion centre of this paternal haplogroup. This lineage is concentrated in the Liu clan (刘姓) of Han populations and may have originated in the Tuge tribe (屠各) of Xiongnu populations. The initial expansion (∼2,600 years ago) and the second phase of expansion (∼1,570 years ago) of haplogroup C2a-M48-F8472 coincide with the earlier appearance and later disappearance of the Tuge tribe. As a sub-clade of M48, the history of F8472 suggested that ancient peoples related to Tungusic-speaking populations were intricately connected with the demographic history of populations in the Mongolian Plateau. Conclusion The appearance of this paternal line in the Han population is helpful for understanding the mixed history of ancient and modern people in the Mongolian Plateau and Central China.

Genetic Identification of Putative Hybrids Between Grey Wolf and Golden Jackal

We describe the results of genetic analysis of 11 phenotypically deviant individuals of grey wolf (Canis lupus Linnaeus, 1758) sensu lato collected in Voronezh State Nature Biosphere Reserve (Chernozem zone of European Russia) and Dagestan (Northern Caucasus, Russia) putatively identified morphologically as hybrids between grey wolf and golden jackal (Canis aureus Linnaeus, 1758). By means of maternally inherited mtDNA (sequences of cytochrome b gene fragment) and paternal lineage markers ZfY no F1 wolf-jackal hybrids were identified. As well, possibility of classification of the studied individuals to next generation hybrids from crosses between different wolf-jackal F1s. However, attribution of these animals to complex hybrids such as various backcrosses cannot be rejected. From the results of analysis by a set of autosomal microsatellite loci we putatively diagnosed a single F2 hybrid. As well, we obtained data that can be considered as traces of hybridization between wolf and jackal in southern regions of European Russa, albeit direct indications of introgression between these species not found. At the same time, the results of both genetic and craniological studies could be interpreted as indication to hybridization between wolves and domestic dogs on the same territories.

Comparison of commercial targeted amplicon sequencing assays for human remains identification casework.

Targeted amplicon sequencing (TAS) facilitates the genotyping of forensically informative single nucleotide polymorphisms (SNPs) using massively parallel sequencing (MPS). For human remains identification, where any extracted DNA is likely to be degraded, TAS may succeed when short tandem repeat (STR) profiling using capillary electrophoresis fails. Further, as well as yielding identity information, SNPs can provide information about ancestry, phenotype, kinship and paternal lineage (Y chromosome haplotypes). Two TAS platforms were compared in this study: Ion AmpliSeq™ panels coupled with Ion Torrent sequencing on an Ion GeneStudio™ S5 Plus System, manufactured by Thermo Fisher Scientific, and the ForenSeq® Kintelligence Kit coupled with Illumina sequencing on the MiSeq FGx® Sequencing System, manufactured by QIAGEN. Four Ion AmpliSeq™ panels (Precision ID Identity, Precision ID Ancestry, DNA Phenotyping and HID Y-SNP) share 177 SNPs with the ForenSeq® Kintelligence Kit and all five were used to profile the DNA extracted from the petrous part of the temporal bone from six skeletonised cadavers. Of the 6 × 177 = 1,062 SNP genotype comparisons, 1,055 (99%) were concordant between the Ion AmpliSeq™ panels and Kintelligence Kit. Of the seven (< 1%) non-concordant SNPs, only three of them (0.3%) would have resulted in erroneous genotypes being reported as a result of allele dropout by either assay, using our optimised relative variant frequency windows for allele calling. We conclude that both the Ion AmpliSeq™ panels and the ForenSeq® Kintelligence Kit were suitable for TAS applied to the human remains in this study.

Genetic diversity and polymorphism of genes associated with meat quality and growth traits of A Luoi Yellow cattle in Vietnam

Background and Aim: A Luoi Yellow cattle is an indigenous cattle breed that is raised in the A Luoi District, Vietnam, characterized by its small body size, high adaptability, and meat quality favored by domestic consumers. Marker-assisted selection is an effective approach for improving breeding genetics and sustainably developing livestock production. Therefore, this study aimed to investigate the genetic diversity and polymorphism of genes associated with meat quality and productivity in the A Luoi Yellow cattle population with the goal of future breeding selection and sustainable development of the A Luoi Yellow beef brand. Materials and Methods: In this study, we genotyped six functional genes, including Leptin (LEP), Calpastatin (CAST), Calpain 1, pleomorphic adenoma gene 1, Sirtuin 1, and Sirtuin 2 (SIRT2), involved in meat quality and growth traits using polymerase chain reaction (PCR) or PCR-restriction fragment length polymorphis. We also investigated mitochondrial DNA (mtDNA) and the Y chromosome-specific gene on the Y chromosome to elucidate the genetic diversity and paternal and maternal origin of the A Luoi Yellow cattle using Sanger sequencing. Results: The results showed that A Luoi yellow cattle have Bos indicus origin from both paternal and maternal lineages. By mtDNA analysis, we identified two new haplotypes of the I1 haplogroup that were not previously detected. The genotyping of the six functional genes indicated that A Luoi Yellow cattle carry favorable alleles that increase meat tenderness and body size, with frequencies of 0.02–0.40. In particular, the presence of desirable homozygous genotypes of the CAST, LEP, and SIRT2 genes will be important for the future selection of animals based on their potential performance in meat quality and productivity. Conclusion: The findings of this study is useful for the future breeding and sustainable development of A Luoi Yellow cattle. Keywords: A Luoi yellow cattle, growth trait, indels, meat tenderness, single nucleotide polymorphisms.

Traces of Bronze Age globalization in East Asia: Insights from a revised phylogeography of the Y-chromosome haplogroup Q1a1a-M120.

In this study, we aim to explore the genetic imprint of Bronze Age globalization in East Asia from a phylogeographic perspective by examining the Y-chromosome haplogroup Q1a1a-M120, and to identify key demographic processes involved in the formation of early China and the ancient Huaxia people. Over the past few decades, we have collected the sequences of 347 Y chromosomes from the haplogroup Q1a1a-M120. These sequences were utilized to analyze and reconstruct a highly revised phylogenetic tree with age estimates. And we analyzed the geographical distribution and spatial autocorrelation of nine major sub-branches of Q1a1a-M120. Finally, we observed the expansion of Q1a1a-M120 from the beginning of the Bronze Age in East Asia, along with the continuous dissemination of its sub-lineages among East Asian populations. We suggest that certain sub-lineages played a significant role in the formation of states and early civilizations in China, as well as in the development of the ancient Huaxia people, who are the direct ancestors of the Han population. Overall, we propose that haplogroup Q-M120 played a role in the introduction of Bronze Age culture to the central region of East Asia. Therefore, it is haplogroup Q-M120, rather than the Western Eurasian paternal lineage, that expanded and contributed to the gene pool of the East Asian population. In summary, the globalization of the Bronze Age led to large-scale population replacement and admixture across various regions of Eurasia; our findings highlight the unique demographic processes that occurred in East Asia during this period.

Long-term effects of grandparental child neglect on adult grandchildren's mental health: A three-generation study

Child neglect is a significant social problem with severe consequences for individuals and society. This study explores how intergenerational transmission of grandparental child neglect affects grandchildren's mental health in adulthood. We utilize a three-generational dataset from the Tromsø Study and estimate a linear probability model to find the distinct roles of both maternal and paternal grandparents. We test the additive risk hypothesis for continuous, intergenerational effects of child neglect in both the maternal and paternal lineages. Furthermore, we use structural equation modeling to test how sequential exposures to neglect across generations ultimately bear on adult mental health outcomes. Our results confirm the additive risk hypothesis but only for maternal grandparents: our findings show that only maternal parents' neglectful parenting is associated with an increased probability of depression in their grandchildren, conditional on whether their parents neglected them. These results contribute to research on intergenerational transmission by the finding that additive risks of child maltreatment flow down generations mainly through maternal lineages.

Understanding Rhododendron intraspecific compatibility in botanic garden collections for species conservation

Context Controlled pollination is an important technique for maintaining intraspecific diversity in integrated plant conservation practices, particularly in genera such as Rhododendron, where open pollination usually produces hybrids with unknown paternal lineages. Aims This study investigated the capacity for viable seed set from self- and intraspecific cross-pollination for Rhododendron taxa in different categories of the International Union for Conservation of Nature (IUCN) Red List, to guide conservation management of threatened species in botanic garden collections. Methods The following five taxa of subsection Maddenia were studied: R. dalhousiae var. dalhousiae (Least Concern), R. dalhousiae var. rhabdotum (Vulnerable), R. lindleyi (Least Concern), R. nuttallii (Near Threatened), and R. excellens (Vulnerable). Controlled pollination was performed on selected garden accessions, and seed germination was tested at an alternating temperature regime of 15/25°C, 8 h photoperiod, and ~6 μmol m−2 s−1 photosynthetic photon flux density (PPFD). Key results Intraspecific compatibilities varied among different taxa and between self- and outcross treatments. X-ray images for Rhododendron seeds showed low capacity to predict seed germination. Neither X-ray scan nor fungicide (Ridomil) treatment showed any adverse impact on seed germination, which has positive implications for seed-banking and subsequent raising of Rhododendron seedlings. Conclusions Controlled intraspecific pollination can be used to maintain diversity of ex situ accessions for selected Rhododendron species. However, the zero or low compatibility demonstrated in some species, such as R. excellens, suggests that these species may require a different approach. Implications Intraspecific pollination should be evaluated for each Rhododendron species before a propagation program is initiated in ex situ conservation.

Two Y‐chromosomal lineages in White‐cheeked macaque (Macaca leucogenys) indicate a possible male‐mediated introgression in ‘sinica’ group macaques

AbstractAimWhether widespread gene flow among primates is emblematic of their initial radiation or resulted from secondary contactremains a long‐standing question. We address this question on ‘sinica’ group macaques, highlighting the origin of the white‐cheeked macaque (Macaca leucogenys).LocationEastern Himalayan highlands of Arunachal Pradesh, India.TaxonMacaca leucogenys Li, Zhao, Fan, 2015b (Cercopithecidae).MethodsMitochondrial genomes and Y‐chromosomal TSPY gene sequences of WCM were obtained from two distant populations through low‐depth genome sequencing. Phylogenetic analyses were conducted along with sequences of other available species within the genus Macaca.ResultsWe observed the presence of a single maternal lineage but two parental lineages. Interestingly, one paternal lineage of the white‐cheeked macaque clustered with a common lineage of M. assamensis and M. munzala. The other paternal lineage clustered with the sequences of the white‐cheeked macaque from the type locality in Southeastern Tibet.Main ConclusionsThe result indicates a possible historic male‐mediated introgression in the white‐cheeked macaque, which is also present in the two other species belonging to the ‘sinica’ group. Therefore, extensive gene flow in ‘sinica’ group macaques possibly came from one or more introgression events in the past that also played a role in the origin and evolution of these macaque species.

Characterizing the Phan Rang Sheep: A First Look at the Y Chromosome, Mitochondrial DNA, and Morphometrics.

The Phan Rang sheep, considered the sole indigenous breed of Vietnam, are primarily concentrated in the two central provinces of Ninh Thuan and Binh Thuan, with Ninh Thuan accounting for more than 90% of the country's sheep population. These provinces are known for their high temperatures and frequent droughts. The long-standing presence of the Phan Rang sheep in these regions suggests their potential resilience to heat stress-a trait of increasing interest in the face of global climate change. Despite the breed's significance, a critical knowledge gap hinders conservation and breeding programs. To address this, our study employed a two-pronged approach. First, we collected body conformational data to aid in breed identification. Second, we analyzed mitochondrial DNA (D-loop) and Y chromosome markers (SRY and SRYM18) to elucidate the maternal and paternal lineages. Among the 68 Phan Rang sheep analyzed for their D-loop, 19 belonged to mitochondrial haplogroup A, while 49 belonged to haplogroup B. The haplogroups can be subdivided into 16 unique haplotypes. All 19 rams surveyed for their paternal lineages belonged to haplotypes H5 and H6. These findings strongly support the hypothesis of dual origins for the Phan Rang sheep. This study presents the first genetic data for the Phan Rang breed, providing crucial insights for future research and conservation efforts.

Impact of patrilocality on contrasting patterns of paternal and maternal heritage in Central-West Africa

Despite their ancient past and high diversity, African populations are the least represented in human population genetic studies. In this study, uniparental markers (mtDNA and Y chromosome) were used to investigate the impact of sociocultural factors on the genetic diversity and inter-ethnolinguistic gene flow in the three major Nigerian groups: Hausa (n = 89), Yoruba (n = 135) and Igbo (n = 134). The results show a distinct history from the maternal and paternal perspectives. The three Nigerian groups present a similar substrate for mtDNA, but not for the Y chromosome. The two Niger–Congo groups, Yoruba and Igbo, are paternally genetically correlated with populations from the same ethnolinguistic affiliation. Meanwhile, the Hausa is paternally closer to other Afro-Asiatic populations and presented a high diversity of lineages from across Africa. When expanding the analyses to other African populations, it is observed that language did not act as a major barrier to female-mediated gene flow and that the differentiation of paternal lineages is better correlated with linguistic than geographic distances. The results obtained demonstrate the impact of patrilocality, a common and well-established practice in populations from Central-West Africa, in the preservation of the patrilineage gene pool and in the affirmation of identity between groups.

Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage.

Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations.

Chasing shadows: Investigating X chromosome mediation in late-onset Alzheimer’s disease

Alzheimer&amp;rsquo;s disease (AD) is a major cause of dementia. While maternal inheritance has been recognized for late-onset AD (LOAD), risk factors have not been identified consistently on the X chromosome. We recently developed a new method to identify an apparent risk of 70% mediated by the X chromosome in newly-presenting cognitive disorders clinic patients with amnestic mild cognitive impairment (aMCI) or early LOAD with unilateral parental lineage for AD or dementia. We sought to confirm our preliminary findings in the Utah Population Database (UPDB). We obtained previously published aggregate data on the risk of AD in the UPDB based on family history, stratified the data by the sex of the proband, and analyzed them using the new method. The X chromosome-attributable relative risk was estimated by calculating the following: Odds ratio (OR) = (women with paternal lineage: Women with maternal lineage)/(men with paternal lineage: Men with maternal lineage). The proportion of genetic risk attributable to the X chromosome is equal to (OR-1)/OR. The analysis did not reveal any risk mediated by the X chromosome, and the null result could be attributed to methodological limitations. Factors that impact the initial or early presentation (incidence) of LOAD, which are appropriate for consideration as risk factors, may not be detectable in a (prevalent) population of deceased individuals. Thus, epidemiological evidence for the contribution of the X chromosome to the development of LOAD will need to be sought prospectively in incident patient populations with newly diagnosed, biologically-confirmed aMCI or LOAD.

Thirty years of conservation breeding: Assessing the genetic diversity of captive Livingstone's fruit bats.

Fruit bats (genus Pteropus) are typically island-endemic species important in seed dispersal and reforestation that are vulnerable to increased extinction risk. An effective method of reducing extinction risk in vulnerable species that cannot be conserved in their native habitat is establishing an ex-situ captive breeding programme. Due to anthropogenic threats and low population numbers, in the early 1990s, a captive breeding programme was established at Jersey Zoo, British Isles, for Critically Endangered Livingstone's fruit bats (Pteropus livingstonii). Here we use six polymorphic microsatellite loci to assess genetic diversity in the captive breeding population of Livingstone's fruit bats (P. livingstonii), 30 years after the programme's establishment, investigating change over generations and comparing our findings with published data from the wild population. We found no significant difference between the genetic diversity in the captive and wild populations of Livingstone's fruit bats (P. livingstonii), in both expected heterozygosity and allelic richness. The captive population has retained a comparable level of genetic diversity to that documented in the wild, and there has been no significant decline in genetic diversity over the last 30 years. We advise that a full pedigree of the paternal lineage is created to improve the management of the captive breeding programme and further reduce the possibility of inbreeding. However, it appears that the captive breeding programme is currently effective at maintaining genetic diversity at levels comparable to those seen in the wild population, which suggests reintroductions could be viable if genetic diversity remains stable in captivity.

Reinterpretasi Hukum Islam terhadap Pembagian Warisan Bagi Anak Pasca Kematian Orang Tua

In the modern era, social dynamics continue to develop, including in terms of inheritance distribution. The issue of dividing inheritance for children after the death of parents is increasingly complex, with various factors that need to be considered. This journal aims to answer and analyze the comparison of the inheritance process for GS as an only child upon the death of both parents according to the Islamic legal system that applies in Indonesia and ensure that Islamic law remains relevant and in accordance with the needs of children in modern times. This journal uses a qualitative approach with literature study methods and critical analysis. Data is collected from various sources, including scientific journals, news articles, and research reports. Research findings show that the distribution of inheritance to children after the death of parents is influenced by various factors, such as social norms, culture, religion and law. This journal refers to efforts to reinterpret Islamic law regarding the distribution of inheritance to children after the death of parents by considering the current social, cultural and political context. Current social dynamics, such as changes in family structure, individualism, and globalization, also influence the inheritance distribution process. The division of inheritance in this journal takes a deeper look at inheritance rights to GS. The condition of GS, who is still a child, is not legally competent to take legal action. In this case, GS's grandfather and grandmother from BA are the guardians based on the paternal lineage attached to them who are the guardians. Further research is needed to understand the complexity of inheritance division in different social contexts. It is necessary to provide education and outreach to the public about the importance of proper inheritance planning and in accordance with applicable social norms and Islamic law.

Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies.

Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.

Y-STR analysis of highly degraded DNA from skeletal remains over 70years old.

The goal of the following study is to clarify whether the skeletal remains over 70years old from missing persons and their alleged relatives shared identical Y-STR loci. Nowadays, advances in ancient DNA extraction techniques and approaches of using multiple different Y-STRs have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Given the ages and conditions of the skeletal remains, ancient DNA extraction methods can be used to maximize the probability of DNA recovery. Considering that information about distant relatives is more relevant for long-term missing persons and alleged family members are male, Y-STR loci analysis is considered the most appropriate and informative approach for determining paternal lineage relationship. In this study, Y-STR genotypes obtained from these alleged relatives were identical to each other and to the alleles of missing persons' consensus profiles at more than 22 loci examined, whilst not being found in Y-STR population database from Y-Chromosome STR Haplotype Reference Database. Therefore, Missing Person No.7 and Missing Person No.18 have a patrilineal relationship with reference samples from Family1 and Family2, respectively. In addition, the fact that Y-STR haplotypes obtained from skeletal remains of missing persons and reference samples are not found in the Han Chinese people from East Asian demonstrates its rarity and further supports a paternal lineage relationship amongst them.

Cultural persistence and the 'herbal medicine paradox': Evidence from European data.

The use of herbal or traditional medicines has survived the proliferation of modern medicine. The phenomenon has been labeled as the 'herbal medicines paradox' (HMP). We study whether such HMP hypothesis can be explained by the persistence of attitudes across cultural boundaries. We undertake a secondary analysis of individual-level migration data to test the persistence of the use of herbal medicines in relation to norms in the person's country of birth (or home country). We study the association between attitudes towards herbal medicine treatments of both first (N = 3630) and second-generation (N = 1618) immigrants in 30 European countries, and the average attitudes of their sending country origins. We find robust evidence of an association that is stronger for the second-generation migrants. We document a stronger effect among maternal than paternal lineages, as well as significant heterogeneity based on migrants' country of origin. Our estimates are robust to different sample analysis. Our estimates are consistent with a cultural explanation for the HMP.

Forensic parameters of 10 Y-STR markers in the Nigerian Hausa, Igbo, and Yoruba populations

Y chromosome short tandem repeats, or Y-STRs, are interesting genetic markers suitable for identifying male offenders in forensic investigations because of the haploid nature of the human male determining chromosome. Furthermore, due to the non-recombining nature of the Y chromosome, Y-STRs are choice markers in paternity or kinship analysis, human evolutionary investigations, and population studies. The lack of reference Y-haplotype data for the populace currently hampers the use of these markers in forensic applications in Nigeria. In this study, the 10 Y-STR loci in the UniQTyperTM Y-10 system including DYS385ab, DYS447, DYS449, DYS481, DYS504, DYS518, DYS612, DYS626, DYS644 and DYS710 were studied in 461 males comprising 139 Hausa, 96 Igbo and 226 Yoruba ethnic populations. Sixty alleles were recorded for the pooled dataset across the 10 loci, with allele frequencies ranging from 0.0022 to 0.6052. There were 430 haplotypes detected, 403 unique (singletons), and 27 were shared. The discrimination capacity and haplotype diversity were 0.9330 and 0.9770, respectively. Allelic richness was highest in the locus DYS626 and lowest in DYS504. Private alleles were found in each group, with the Hausa population having the highest number. Duplications and microvariant alleles were also reported. These findings may be helpful for paternal lineage investigations, population genetics, and forensic applications among the Nigerian populations.

Shrouded in history: Unveiling the ways of life of an early Muslim population in Santarém, Portugal (8th- 10th century AD).

In around 716 AD, the city of Santarém, Portugal, was conquered by the Berber and Arab armies that swept the Iberian Peninsula and went on to rule the region until the 12th century. Archaeological excavations in 2007/08 discovered an Islamic necropolis (Avenida 5 de Outubro #2-8) that appears to contain the remains of an early Muslim population in Santarém (8th- 10th century). In this study, skeletal material from 58 adult individuals was analysed for stable carbon (δ13Ccol; δ13Cap), nitrogen (δ15N) and sulphur (δ34S) isotope ratios in bones, and stable oxygen (δ18O), carbon (δ13Cen) and radiogenic strontium (87Sr/86Sr) isotopes in tooth enamel. The results of this study revealed a dietary pattern of predominantly C3-plant and domestic C3-fed herbivore consumption during adulthood (δ13Ccol and δ15N, respectively) but a higher proportion of C4-plant input during childhood (δ13Cen) for some individuals-interpreted as possible childhood consumption of millet porridge, a common practice in North Africa-in those with unorthodox burial types (Groups 1 and 2) that was not practiced in the individuals with canonical burials (Group 3). In this first mobility study of a medieval Muslim population in Portugal, δ18ODW values revealed greater heterogeneity in Groups 1 and 2, consistent with diverse origins, some in more humid regions than Santarém when compared to regional precipitation δ18O data, contrasting the more homogenous Group 3, consistent with the local precipitation δ18O range. Ancient DNA analysis conducted on three individuals revealed maternal (mtDNA) and paternal (Y-chromosome) lineages compatible with a North African origin for (at least) some of the individuals. Additionally, mobility of females in this population was higher than males, potentially resulting from a patrilocal social system, practiced in Berber and Arab communities. These results serve to offer a more detailed insight into the ancestry and cultural practices of early Muslim populations in Iberia.

Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1–1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.