Maternal Lineages Research Articles

The Dogs of Tsenacomoco: Ancient DNA Reveals the Presence of Local Dogs at Jamestown Colony in the Early Seventeenth Century

Abstract Multiple studies have demonstrated that European colonization of the Americas led to the death of nearly all North American dog mitochondrial lineages and replacement with European ones sometime between AD 1492 and the present day. Historical records indicate that colonists imported dogs from Europe to North America, where they became objects of interest and exchange as early as the seventeenth century. However, it is not clear whether the earliest archaeological dogs recovered from colonial contexts were of European, Indigenous, or mixed descent. To clarify the ancestry of dogs from the Jamestown Colony, Virginia, we sequenced ancient mitochondrial DNA from six archaeological dogs from the period 1609–1617. Our analysis shows that the Jamestown dogs have maternal lineages most closely associated with those of ancient Indigenous dogs of North America. Furthermore, these maternal lineages cluster with dogs from Late Woodland, Hopewell, and Virginia Algonquian archaeological sites. Our recovery of Indigenous dog lineages from a European colonial site suggests a complex social history of dogs at the interface of Indigenous and European populations during the early colonial period.

BIOINFORMATICS AND MOLECULAR ANALYSES IDENTIFIED THE CONTROL REGION AS THE MOST POWERFUL MITOGENOMIC MARKER FOR DISTINGUISHING THE MAIN MATERNAL HAPLOGROUPS IN GOATS

Identification of genetic markers to distinguish animals within and between species demands extensive genomic and bioinformatics investigation. Previous studies have not carefully taken into consideration the effect of mitogenomic components on the genetic differentiation of the maternal lineages in goats. As a precaution, the complete goat mitogenome was downloaded from the NCBI database and used in the current study to assess the effects of the choice of mitogenomic fragments on phylogenetic studies and to identify any potential polymorphic region by which the main maternal haplogroups of goats can be classified. Phylogenetic results confirmed that all 13 individual mitochondrial protein-coding genes and 2 ribosomal genes are not applicable to differentiate the maternal lineages. Instead, a single novel polymorphic region with a length of 756 bp within the control region was successfully amplified by newly designed primers. Both phylogenetic analysis and principal components analysis of the sequenced mitogenomic region of the mtDNA control region efficiently differentiated the main maternal haplogroups in goats. Higher numbers of polymorphic sites were found in the control region and the mitogenomic marker region. Highly significant correlations were discovered between the polymorphic sites and the length of each individual mitogenomic component. Our results demonstrate useful guidance and cautionary notes for researchers who are interested in the investigation of genetic diversity in animal species using mtDNA sequences. The bioinformatics and molecular methods used herein can be powerful in selecting a minimum amount of data using PCR amplification when the entire sequences of the mitogenome are unavailable.

New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages

Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.

Developmental origins of exceptional health and survival: A four-generation family cohort study.

Previous researched has demonstrated potent health and survival advantages across three-generations in longevity-enriched families. However, the survival advantage associated with familial longevity may manifest earlier in life than previously thought. We conducted a matched cohort study comparing early health trajectories in third-generation grandchildren (n = 5,637) and fourth-generation great-grandchildren (n = 14,908) of longevity-enriched sibships to demographically matched births (n = 41,090) in Denmark between 1973 and 2018. Lower risk was observed across a range of adverse early life outcomes in the grandchildren, including infant mortality (Hazard Ratio (HR) = 0.53, 95% CI [0.36, 0.77]), preterm birth (Odds Ratio (OR) = 0.82, [0.72, 0.93]), small for gestational age (OR = 0.83, [0.76, 0.90]) and neonatal respiratory disorders (OR = 0.77, [0.67, 0.88]). Relative advantages in parental education and maternal smoking were observed in both generations to a similar degree. However, a much smaller reduction in infant mortality was observed in the great-grandchildren (HR = 0.90, [0.70, 1.17]) and benefits across other outcomes were also less consistent, despite persisting socioeconomic and behavioural advantages. Lastly, maternal, and paternal lines of transmission were equipotent in the transmission of infant survival advantages. Descendants of longevity-enriched sibships exhibit a broad health advantage manifesting as early the perinatal period. However, this effect is strongly diluted over successive generations. Our findings suggest that exceptional health and survival may have early developmental components and implicate heritable genetic and or epigenetic factors in their specific transmission. Previous researched has demonstrated potent health and survival advantages across three-generations in longevity-enriched families. However, the survival advantage associated with familial longevity may manifest earlier in life than previously thought.In our study of third and fourth-generation descendants of longevity-enriched sibships, we observed a broad infant health and survival advantage reflected by protection against a diverse range of adverse birth outcomes.These advantages were strongly attenuated between the third and fourth generations, independent of otherwise stable socioeconomic and behavioural parental advantages, as well as maternal and paternal lines of transmission.Our findings suggest that familial aggregation of exceptional health and survival may have early life developmental components and triangulate to implicate heritable genetic and or epigenetic factors in their transmission.

20 Effects of a stabilized fish oil on boar semen quality when fed during summer months

Abstract The objective of this study was to investigate the effects of feeding a stabilized fish oil source to different genetic lines on boar semen quality. A total of 127 boars representing three genetic lines (PIC 337, PIC 800, and PIC L03; Hendersonville, TN) at a commercial boar stud were balanced by age, body condition, and previous semen quality and randomly allotted to one of two dietary treatments within genetic line. Boars were assigned to either receive Control; a daily top dress of 32g of corn starch; or Fish oil; a daily top dress of 32g of Salmate DHA+ (The Ballard Group, 2407 Ashland Ave., Cincinnati, OH 45206 USA) to provide 2.38 g of docosahexaenoic acid (DHA). The top-dress supplementation was provided by placing it on top of the daily ration of feed for each individual boar on the floor once each day immediately after their feed has been delivered to them. Supplementation lasted for 16 wk from June-September, 2023 during which weekly semen collection was performed. Semen was evaluated at the stud for concentration and motility parameters using computer assisted semen analysis. Data was analyzed using generalized linear mixed models with the lmer and glmer functions of R. Boar was the experimental unit, with dietary treatment, genetic line, and their interaction tested as fixed effects while age at collection served as a covariate. Boar nested within treatment combinations was used as a random effect to account for repeated measurements within the same boar. There was no evidence (P > 0.10) for dietary treatment by genetic line interaction for any response criteria (Table 1). There was no evidence of fish oil supplementation effects (P > 0.10) on semen volume, concentration, total sperm cells per ejaculate, percentage of accepted ejaculates, or number of doses produced per accepted ejaculate. There was no evidence of fish oil supplementation effects (P > 0.10) on percentage motile sperm cells, or percentage of proximal and distal droplets and abnormal tails. Line 800 boars had the least (P < 0.05) semen volume, but greatest (P < 0.05) sperm concentration, resulting in no evidence for differences (P > 0.10) between the three genetic lines in total sperm cells per ejaculate. Line 03 boars had increased (P < 0.05) percentage of rejected ejaculates as well as decreased number of doses produced per accepted ejaculate (P < 0.05) compared with lines 337 and 800 boars. There was no evidence for differences (P > 0.10) in sperm motility, proximal and distal droplets, or abnormal tails between the three genetic lines. In summary, maternal line boars had an increased proportion of rejected ejaculates per boar and a decreased number of doses produced compared with terminal line boars. Feeding a stabilized fish oil to provide 2.38 g of DHA did not improve semen during summer months.

Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity

BackgroundDespite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant Arabidopsis thaliana in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity.ResultsLow and high genotypic and ecological diversity was found in edge and core Iberian environments, respectively. Given that selection is expected to be stronger in edge environments and that ecological diversity may enhance both phenotypic variation and plasticity, we expected genotypic diversity to be positively associated with phenotypic variation and plasticity. However, maternal lines, irrespective of the genotypic and ecological diversity of their population of origin, exhibited a substantial amount of phenotypic variation and plasticity for all traits. Furthermore, all populations harbored maternal lines with canalization (robustness) or sensitivity in response to harsher environmental conditions in one of the two experiments.ConclusionsOverall, we conclude that the environmental attributes of each population probably determine their genotypic diversity, but all populations maintain substantial phenotypic variation and plasticity for all traits, which represents an asset to endure in changing environments.

Effect of transgenerational diabetes via maternal lineage in female rats

AimTo investigate the transgenerational effect of maternal hyperglycemia on oxidative stress markers, lipid profile, glycemia, pancreatic beta (β)-cells, and reproductive outcomes in the F2 adult generation. Additionally, to expand the knowledge on transgenerational diabetes the F3 generation at birth will be evaluated. MethodsOn day 5 of postnatal life female Sprague-Dawley rat newborns (F0 generation) were distributed into two groups: Diabetic (Streptozotocin-STZ, 70 mg/kg body weight, subcutaneous route) and Control rats. Adult female rats from the F0 generation and subsequently the F1 generation were mated to obtain the F2 generation, which was distributed into F2 generation (granddaughters) from control (F2_C) and diabetic (F2_D) rats. Oral Glucose Tolerance Test (OGTT), the area under the curve (AUC), blood biochemical analyses, and pancreatic morphology were analyzed before pregnancy. Reproductive outcomes were performed at the end of pregnancy. At birth, the glycemia and body weight of F3_C and F3_D rats were determined. p < 0.05 was considered significant. ResultsF2_D had higher body weight, triglyceride levels, and percentage of insulin-immunostained cells, contributing to glucose intolerance, and insulin resistance before pregnancy. At day 21 of pregnancy, the F2_D showed increased embryonic losses before and after implantation (84.33 and 83.74 %, respectively). At birth, F3_D presented hyperglycemia, and 16.3 % of newborns were large for pregnancy age (LGA). ConclusionDiabetes induction since the neonatal period in the first generation (F0) led to transgenerational (F2 and F3 generations) changes via the maternal lineage of female rats, confirming the relevance of control strictly the glycemia all the time.

Genetic parameters for mesenteric torsion in a pig maternal line

Mesenteric torsion (MT) is a condition characterized by the twisting of intestinal loops, leading to a disruption in blood flow and abdominal distension. Several factors can predispose animals to this condition, which primarily affects healthy, fast-growing pigs and often results in fatal outcomes. Given the absence of studies on the genetic factors associated with this condition, our research aimed to estimate the heritability coefficient for MT and explore the genetic correlations between MT and performance traits in pigs. Our dataset comprised of 43,384 records of pigs from a maternal line from a nucleus farm. These pigs were born between 2010 and 2022 and had recorded information regarding MT status (0 for healthy and 1 for affected animals), weaning weight (WW), as well as pedigree, genotypes, and genomic estimated breeding values (GEBVs) for the following traits: MT status, days to reach 110 kg (D110), feed conversion adjusted to 110 kg (FC110), and backfat thickness adjusted to 110 kg (BT110). In our statistical model, the effects of contemporary group (CG: sex, year, and week of weaning) and the linear covariate WW were considered fixed effects, while the direct additive genetic effect was accounted as random. On average, pigs affected by MT had an age of 104.35 ± 37.75 days, and the condition had an overall herd frequency of 2.46 %. Mesenteric torsion occurred more frequently in female pigs raised in collective pens compared to non-castrated males raised in individual pens. Heritability estimates for MT, using both pedigree (0.13 ± 0.02) and genomic (0.12 ± 0.02) data, were of low magnitude. This suggests that while there is genetic variability associated with MT, a significant portion of this variation is due to environmental variance. The correlation between MT and BT110 GEBVs was of low magnitude (0.05). In contrast, the correlations between GEBVs for MT and both D110 and FC110 were moderate in magnitude (0.22 for both traits). This implies that pigs taking longer to reach 110 kg and those with poorer feed conversion are more likely to develop MT. There is genetic variability for mesenteric torsion in pigs. Selection aimed at improving feed conversion and reducing the age at which pigs reach 110 kg could lead to a decrease in the occurrence of MT within pig populations.

Unravelling the maternal evolutionary history of the African leopard (Panthera pardus pardus).

The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.

Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach

The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.

Microbiome composition as a potential predictor of longevity in rabbits

BackgroundLongevity and resilience are two fundamental traits for more sustainable livestock production. These traits are closely related, as resilient animals tend to have longer lifespans. An interesting criterion for increasing longevity in rabbit could be based on the information provided by its gut microbiome. The gut microbiome is essential for regulating health and plays crucial roles in the development of the immune system. The aim of this research was to investigate if animals with different longevities have different microbial profiles. We sequenced the 16S rRNA gene from soft faeces from 95 does. First, we compared two maternal rabbit lines with different longevities; a standard longevity maternal line (A) and a maternal line (LP) that was founded based on longevity criteria: females with a minimum of 25 parities with an average prolificacy per parity of 9 or more. Second, we compared the gut microbiota of two groups of animals from line LP with different longevities: females that died/were culled with two parities or less (LLP) and females with more than 15 parities (HLP).ResultsDifferences in alpha and beta diversity were observed between lines A and LP, and a partial least square discriminant analysis (PLS-DA) showed a high prediction accuracy (> 91%) of classification of animals to line A versus LP (146 amplicon sequence variants (ASV)). The PLS-DA also showed a high prediction accuracy (> 94%) to classify animals to the LLP and HLP groups (53 ASV). Interestingly, some of the most important taxa identified in the PLS-DA were common to both comparisons (Akkermansia, Christensenellaceae R-7, UnculturedEubacteriaceae, among others) and have been reported to be related to resilience and longevity.ConclusionsOur results indicate that the first parity gut microbiome profile differs between the two rabbit maternal lines (A and LP) and, to a lesser extent, between animals of line LP with different longevities (LLP and HLP). Several genera were able to discriminate animals from the two lines and animals with different longevities, which shows that the gut microbiome could be used as a predictive factor for longevity, or as a selection criterion for these traits.

Genetic identification of human remains from the Korean War.

The genetic identification of skeletal remains from Chinese People's Volunteers (CPVs) of the Korean War has been challenging because of the degraded DNA samples and the lack of living close relatives. This study established a workflow for identifying CPVs by combining Y-chromosome short tandem repeats (Y-STRs), mitochondrial DNA (mtDNA) hypervariable regions I and II, autosomal STRs (aSTRs), and identity-informative SNPs (iiSNPs). A total of 20 skeletal remains of CPVs and 46 samples from their alleged relatives were collected. The success rate of DNA extraction from human remains was 100%. Based on Y-STRs, six remains shared the same male lineages with their alleged relatives. Meanwhile, mtDNA genotyping supports two remains sharing the same maternal lineages with their alleged relatives. Likelihood ratios (LRs) were further obtained from 27 aSTRs and 94 iiSNPs or 1936 iiSNPs to confirm their relationship. All joint pedigree LRs were >100. Finally, six remains were successfully identified. This pilot study for the systematic genetic identification of CPVs from the Korean War can be applied for the large-scale identification of CPVs in the future.

Genetic diversity of mitochondrial DNA D-loop sequence in Bang Troi chicken breed

Bang Troi chicken (GBT) is a local chicken that is free-gardening raised in Quang Ninh province. A 1,268 bp of mitochondrial DNA (mtDNA) D-loop of 17 Bang Troi chicken individuals was sequenced and analyzed. Comparative multiple sequence alignment revealed 17 base substitutions within 17 Bang Troi chicken individuals. Bang Troi chicken had a relatively high level of genetic diversity, expressed in the number of 13 haplotypes, haplotype diversity of 0.949. The Tajima’s test indicated that the analysed population in balancing selection with a D-value of 2.39. A phylogenetic tree based on 455 bp of hypervariable mtD-loop sequence classified 17 Bang Troi chicken individuals into three clades A, B, and E, which are common groups of Vietnamese and Asia indigenous chickens. This result provides the first genetic information and maternal lineages of Bang Troi chickens and it can support for registration of local chicken breeds.

Оцінка товарних кондицій помісей першого покоління антонінсько-зозуленецьких та галицьких рамчастих коропів

Purpose. To characterize age-1+ hybrids obtained from the crossing of Galician framed carp (GFC) and Antoniny-Zozulenets framed carp (AZFC) according to a set of commercial conditions in comparison with parental lines. Methodology. The objects of the study were age-1+ hybrids of the reciprocal crossing of Galician and Antoniny-Zozulenets carps grown in pond conditions of the “Karpatskyi Vodogray” LLC. The study was conducted at the end of the growing season according to methodological recommendations. The body of the experimental carp for analysis was divided into its constituent parts: scales, fillet with skin, entrails, fins and bones. In the process of work, blood was removed, its weight was attributed to the entrails. The head was separated from the carcass by breaking it off between the occipital bone and the first vertebra.Each part was weighed separately and presented as a percentage of the total body weight. Findings. The obtained results showed that the yield of the main part of the fillet with skin in crossbred groups of age-1+ carp was 48.7–52.0% and was higher compared to purebred offspring.In comparison with the original maternal line, crossbred age-1+ ♀GFC ×♂AZFC had a higher index of relative fillet weight by 3.15%, and the similar 1.6% superiority was observed in crossbreds ♀AZFC × ♂GFC. At the same time, with an increase in the average weight of age-1+ by 28.9–68.6% in the 2023 studies, the relative weight of the carcass increased by 2.4–11.0%. At the same time, the relative weight of the head decreased by 5.3-6.1%, and the relative weight of the entrails increased by 0.7-4.7%. In general, the inedible part of the studied groups of fish was in the range of 27.2–32.4%. In terms of the yield of fillets per 1 ha of fattening pond, the superiority of interbreeding groups of age-1+ was 31.5–62.7%. The obtained results indicate the expediency of their use as new highly productive commercial lines in pond farms of the Polissiya zone. Originality. For the first time, a comparative analysis of the nutritional value parameters of age-1+ carp from reciprocal crossings of Galician and Antoniny-Zozulenet framed carp and the original pure lines cultivated in the conditions of Ukrainian Polissiya was carried out. Practical value. The obtained results will complement the studies of previous years and will allow providing recommendations on the use of these hybrids for commercial cultivation in the Polissiya zone of Ukraine. Keywords: carp, weight, market conditions, edible and inedible body parts.

Влияние сублетальных доз хлорида кадмия на развитие доимплантационных зародышей в двух поколениях мышей

Cadmium is a heavy metal, highly toxic pollutant, entering the environment as a by-product of most modern industries. The effect of cadmium on the body depends on the route of entry, duration and dose of exposure. One of the important areas of this research is the study of the effect of cadmium on early development, leading to diseases in the adult body and possible developmental abnormalities in offspring. The aim of this study was to analyze the development of preimplantation embryos of mice exposed in utero to cadmium chloride and embryos obtained from cadmium-exposed parents. Preimplantation embryos of F1 (CBA×C57BL) hybrid mice exposed in utero to 30 µM of cadmium chloride (F1 — the first generation) and embryos of similar age, obtained from females and males, exposed in utero (F2 — the second generation), was studied. The toxic effect of cadmium chloride was studied by paternal, maternal and “double” (both parents were exposed) lines of inheritance. The development of embryos was assessed by the rate of blastomeres cleavage and the number of blastocysts. The F1 generation embryos exposed to cadmium chloride in utero passed the initial stages of cleavage and blastocyst formation faster compared to the control embryos. The development of the the maternal line second generation embryos (F2) was comparable with the control group. In the paternal and “double” (both parents were exposed) lines of inheritance, the rate of cleavage at the morula stage was slowdown, however, at the blastocyst stage, the rate of cleavage of embryos did not statistically differ from the control embryos. The effect of sublethal doses of cadmium chloride on famale mice at the onset of pregnancy affects not only the embryos of the first generation, directly exposed to cadmium chloride, but also the descendants of exposed parents in the second generation, slowing down the process of proliferation in the embryos of the paternal line of inheritance and in embryos born from two exposed parents. The results obtained in our model suggest that the harm from smoking caused by the accumulation of cadmium is manifested not only in children, but also in grandchildren. The epigenetic mechanism of such inheritance is most likely, which gives grounds for the development of preventive approaches to eliminate possible harmful consequences. It is advisable to recommend stopping smoking during pregnancy and in the period before conception.

Hybridization in the Subtribe Alopecurinae Dumort. (Poaceae) According to Molecular Phylogenetic Analysis: Different Ploidy Level Tells Different Origin of the Groups.

We performed next-generation sequencing of the 18S rDNA-ITS1-5.8S rDNA region along with traditional Sanger sequencing of rbcL, matK, ndhF, and ITS1-5.8S rDNA-ITS2 to clarify the hybridization pattern in the subtribe Alopecurinae and in the genus Alopecurus in particular. Our data support the hybrid origin of Alopecurus × brachystylus from hybridization between A. geniculatus (sect. Alopecurium) and A. pratensis (sect. Alopecurus). Moreover, in the rDNA of hybrid A. × brachystylus, only A. aequalis-like ribotypes from tetraploid A. geniculatus participated. Surprisingly, we found the traces of introgression of A. arundinaceus-like ribotypes not only in hybrid A. × marssonii (A. geniculatus × A. arundinaceus) but in A. aequalis s. str. as well. A high-polyploid group from the section Alopecurus, A. aggr. alpinus has undoubted hybrid origin: e. g., A. brachystachyus has rDNA from the sect. Alopecurium. Alopecurus alpinus, with its allies, is clearly distinct from other members of the sect. Alopecurus (especially by maternal line) and thus we can re-establish a previous opinion about the separate group to which A. alpinus belongs. Species from the section Colobachne (presumably Alpine grasses from Ancient Mediterranean region) probably hybridized with the A. alpinus group. Even A. myosuroides (sect. Pseudophalaris) that could be referred to the separate genus has ribotypes common with the species of the section Alopecurium (A. aequalis, A. geniculatus) in one of the accessions. Additionally, we found that the possible polyphyletic origin of the genus Limnas. Limnas stelleri is very close to Alopecurus magellanicus according to NGS data, while L. malyschevii is more or less distinct from other studied species of the genus Alopecurus.

Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs.

Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.

Interspecific Sharing of Closely Related Chloroplast Genome Haplotypes among Sclerophyllous Oaks in the Hot-Dry Valley of the Jinsha River, Southwestern China

Evergreen sclerophyllous oak forests (ESOFs) in southwestern China are a special vegetation type developed in response to the expansion of arid habitats after the uplift of the Himalayas. Here, we used chloroplast (cp) DNA and nuclear ribosomal (nr) DNA to investigate the fine-scale genetic variation patterns of six sympatric oaks (Quercus, Fagaceae) in the hot-dry valley ESOFs of the Jinsha River, southwestern China. Three cp genomes were assembled for each species. Nine cp genome haplotypes and 16 nrDNA haplotypes were identified based on single-nucleotide variants and indels. Our results demonstrated that discordance existed between the cpDNA and nrDNA phylogenies of the sclerophyllous oaks in section Ilex. The nrDNA phylogeny was consistent with species boundaries, while the cpDNA phylogeny was decoupled from taxonomy. Interspecific sharing of closely related cp genome haplotypes was detected between Quercus cocciferoides and the other two sclerophyllous oaks, Q. longispica and Q. franchetii. Specifically, Q. cocciferoides and Q. longispica sampled in a mixed stand exhibited two haplotypes that differed by a 9 bp indel. The local distribution of the two highly similar haplotypes suggested that they may have arisen from ancient introgression. Given that the two species have diverged for a long time, it is possible that the ancestral cp genome of one species was captured by another species through asymmetric introgression in early times, and an indel event occurred subsequently. Phylogenetic analyses using more previously published cp genome sequences indicated that Q. cocciferoides and Q. franchetii shared multiple cpDNA lineages of Ilex oaks, which may be caused by shared ancestral polymorphism and/or ancient introgression. Our study showed that at least three highly variable regions (ψycf1, ndhF-rpl32, and trnKUUU-rps16 or rpl32-trnLUAG) can distinguish the nine haplotypes identified by whole-cp genome sequences. These markers are useful for the evolutionary studies of the maternal lineages of oaks in hot-dry valley ESOFs.

Family History in the Iberian Peninsula during Chalcolithic and Bronze Age: An Interpretation through the Genetic Analysis of Plural Burials

Throughout history, it has been observed that human populations have buried the deceased members of their communities following different patterns. During the Copper Age and the Bronze Age—periods on which this study focuses—in the northern sub-plateau of the Iberian Peninsula, we identified different patterns of multiple or collective burial. This work analyzes a total of 58 individuals buried in different multiple or collective graves, to investigate whether the practice of these burials implies a family or biological link between individuals buried together. With this aim, STR markers of nuclear DNA were analyzed, as well as the hypervariable regions I and II of mitochondrial DNA, establishing both close kinship relationships and relationships through maternal lineage. We observed different burial patterns, detecting certain maternal lines preserved in some common burials maintained over time. Close family relationships were observed to a lesser extent, with some occasional exceptions. The results of the analysis formed the basis for a discussion on the concepts of family and community.

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.