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Genome-wide insights into the evolutionary and demographic history of the red alga Mazzaella laminarioides: Evidence for speciation with ancient migration along the southeast Pacific coast.

The mechanisms driving lineage divergence in red algae remain unexplored, despite the group's remarkable diversity and ancient evolutionary history. The red alga Mazzaella laminarioides, a Chilean intertidal species complex composed of three parapatric cryptic lineages (North, Center, South), offers a valuable system to evaluate these processes, as its life history combines severe dispersal limitation with a haploid-diploid cycle that may influence the emergence of reproductive barriers. We reconstructed its evolutionary history using whole-genome sequencing and nuclear genome assembly of representative individuals from each lineage. Phylogenomic analyses based on 1,507 single-copy orthologs recovered three deeply divergent lineages with limited nuclear discordance consistent with incomplete lineage sorting. For both splits, demographic modelling was most consistent with an Ancient Migration scenario, although support over strict isolation was moderate, suggesting that divergence may have begun with low asymmetric ancestral gene flow followed by subsequent loss of connectivity, demographic bottlenecks, and later population expansion. Coding sequence analyses revealed lineage-specific dN/dS heterogeneity; only one South-lineage locus passed FDR correction (metaxin-1, mitochondrial protein import), with two further South-lineage candidates in chlorophyll and heme biosynthesis falling below the FDR threshold. Together, these signals suggest that divergent selective pressures on energy acquisition may have contributed to divergence at the southern end of the distribution. These results add to the small but growing body of whole-genome data for red algae and, alongside recent macroalgal studies, suggest that ancestral connectivity could be a recurrent feature of lineage divergence even in marine organisms with extremely restricted dispersal.

Rhodophyta

Southeast Asian mitochondrial DNA analysis reveals genetic continuity of ancient mongoloid migrations.

Human mitochondrial DNAs (mtDNAs) from 153 independent samples encompassing seven Asian populations were surveyed for sequence variation using the polymerase chain reaction (PCR), restriction endonuclease analysis and oligonucleotide hybridization. All Asian populations were found to share two ancient AluI/DdeI polymorphisms at nps 10394 and 10397 and to be genetically similar indicating that they share a common ancestry. The greatest mtDNA diversity and the highest frequency of mtDNAs with HpaI/HincII morph 1 were observed in the Vietnamese suggesting a Southern Mongoloid origin of Asians. Remnants of the founding populations of Papua New Guinea (PNG) were found in Malaysia, and a marked frequency cline for the COII/tRNA(Lys) intergenic deletion was observed along coastal Asia. Phylogenetic analysis indicates that both insertion and deletion mutations in the COII/tRNA(Lys) region have occurred more than once.

Asia, Southeastern

American Indian prehistory as written in the mitochondrial DNA: a review.

Native Americans have been divided into three linguistic groups: the reasonably well-defined Eskaleut and Nadene of northern North America and the highly heterogeneous Amerind of North, Central, and South America. The heterogeneity of the Amerinds has been proposed to be the result of either multiple independent migrations or a single ancient migration with extensive in situ radiation. To investigate the origin and interrelationship of the American Indians, we examined the mitochondrial DNA (mtDNA) variation in 87 Amerinds (Pima, Maya, and Ticuna of North, Central, and South America, respectively), 80 Nadene (Dogrib and Tlingit of northwest North America and Navajo of the southwest North America), and 153 Asians from 7 diverse populations. American Indian mtDNAs were found to be directly descended from five founding Asian mtDNAs and to cluster into four lineages, each characterized by a different rare Asian mtDNA marker. Lineage A is defined by a HaeIII site gain at np 663, lineage B by a 9-bp deletion between the COII and tRNA(Lys) genes, lineage C by a HincII site loss at np 13259, and lineage D by an AluI site loss at np 5176. The North, Central, and South America Amerinds were found to harbor all four lineages, demonstrating that the Amerinds originated from a common ancestral genetic stock. The genetic variation of three of the four Amerind lineages (A, C, and D) was similar with a mean value of 0.084%, whereas the sequence variation in the fourth lineage (B) was much lower, raising the possibility of an independent arrival. By contrast, the Nadene mtDNAs were predominantly from lineage A, with 27% of them having a Nadene-specific RsaI site loss at np 16329. The accumulated Nadene variation was only 0.021%. These results demonstrate that the Amerind mtDNAs arose from one or maybe two Asian migrations that were distinct from the migration of the Nadene and that the Amerind populations are about four times older than the Nadene.

Asia

Ancient DNA as a temporal lens: reconstructing evolution, migration, and disease dynamics.

Ancient DNA (aDNA) has transformed evolutionary biology and anthropology by providing direct, chronologically validated genetic evidence over millennia. This review synthesizes significant findings from the paleogenomic era (2010-2025), demonstrating how ancient DNA has resolved persistent debates across four interconnected themes: (i) human migration and admixture, revealing complex population transitions from archaic hominins to Holocene expansions; (ii) adaptation, tracking allele frequency changes during domestication and selection; (iii) pathogen history, clarifying the origins of pandemics and the evolution of microbiomes; and (iv) ecosystem dynamics, identifying extinction causes through sedimentary DNA and conservation genomics. We contend that scientific rigor and ethical stewardship are crucial for accurate conclusions, given ancient DNA study requires the destructive collection of culturally significant remains. This review argues that continued advancement will depend on the integration of genomic data with archaeological, isotopic, and proteomic evidence, and highlights the necessity for equitable involvement with descendant communities. By conceptualizing the past as a continuum of dynamic processes rather than static events, ancient DNA provides a revised historical narrative and insights relevant to contemporary concerns in conservation, health, and social justice.

Evolution

Ancient DNA connects large-scale migration with the spread of Slavs.

The second half of the first millennium CE in Central and Eastern Europe was accompanied by fundamental cultural and political transformations. This period of change is commonly associated with the appearance of the Slavs, which is supported by textual evidence1,2 and coincides with the emergence of similar archaeological horizons3-6. However, so far there has been no consensus on whether this archaeological horizon spread by migration, Slavicisation or a combination of both. Genetic data remain sparse, especially owing to the widespread practice of cremation in the early phase of the Slavic settlement. Here we present genome-wide data from 555 ancient individuals, including 359 samples from Slavic contexts from as early as the seventh century CE. Our data demonstrate large-scale population movement from Eastern Europe during the sixth to eighth centuries, replacing more than 80% of the local gene pool in Eastern Germany, Poland and Croatia. Yet, we also show substantial regional heterogeneity as well as a lack of sex-biased admixture, indicating varying degrees of cultural assimilation of the autochthonous populations. Comparing archaeological and genetic evidence, we find that the change in ancestry in Eastern Germany coincided with a change in social organization, characterized by an intensification of inter- and intra-site genetic relatedness and patrilocality. On the European scale, it appears plausible that the changes in material culture and language between the sixth and eighth centuries were connected to these large-scale population movements.

DNA, Ancient

A genetic reconstruction of the history of the population of the Iberian Peninsula.

The genetic patterns detectable in human populations of the Iberian Peninsula are shown by means of 'synthetic genetic maps', i.e. geographic maps of the highest principal components (PC) of gene frequencies. This method of analysis separates independent patterns of the genetic landscape, which hopefully represents different, major evolutionary events of the past. Among these are clines established by ancient important migrations, and local differentiations of populations due to barriers responsible for relative isolation. Only events of some magnitude from a demographic point of view, involving populations having initially definite genetic differences are detectable by the method. For this to be true, the genetic consequences of these events must not have been entirely smoothed out by later, prolonged genetic exchange between neighbours; but simulations have shown that long clines produced by major migrations can be rather stable in time. The first synthetic map, corresponding to the first PC, shows that the major difference in the Iberian Peninsula is that between people originally of Basque and non-Basque descent. The recession in time of the boundaries of the Basque-speaking area seems correlated with the progressive genetic dilution of the Basque genotype in modern populations, as we move away from the centre of the Basque area. Clearly there must have been a close relationship in the progressive loss of the Basque language and increasing genetic admixture with neighbours. Most probably, Basques represent descendants of Paleolithic and/or Mesolithic populations and non-Basques later arrivals, beginning with the Neolithic. The second synthetic map is correlated with early Neolithic infiltrations from the eastern edge of the Pyrenees. It has been shown by archaeologists that, in some areas, early Neolithics lived side by side at overlapping dates with well developed Mesolithics. The demographic impact of Neolithic farmers versus Mesolithics, and therefore their genetic influence was thus less important in the Iberian Peninsula than in Central Europe. The third synthetic map shows a correlation with the linguistic and historical duality between the Atlantic and Mediterranean fringes, which developed in the first millennium B.C. and was probably determined, to some extent, by infiltrations through the Pyrenees of the Urnfield cultural elements as well as by several other later events.

Biological Evolution

[Genetic traits in the area of Bodrogköz].

In 1984 a late malaria endemic area, called Bodrogköz was studied. This was a reexamination of the population genetic work performed by Walter, Nemeskéri. In six villages of Bodrogköz 328 persons were tested for AB0, Rh blood groups, haptoglobins, haemoglobin concentration, haematocrit, erythrocyte amount, the MCV, the MCH and the G-6-PD were analyzed. The quantitative determination of HbF and HbA2, red cell osmotic resistance and thalassemia were measured as well. Thalassemia heterozygote carriers and an increased level of HbF were revealed. The frequency of G-6-PD deficiency was 0.39%. In Bodrogköz the frequencies of AB0, Rh and haptoglobin types were similar in the present and all previous studies. The background of this similarity might be the genetic similarity between two following generations. On the basis of these facts, the Hb0 Arab and partially DNA work we suggested an alternative hypothesis that these mutant genes got into Bodrogköz by the rather later migration than with ancient Hungarian people during the period of conquest of Hungary.

Blood Group Antigens

Ecophysiological hierarchies.

Among bovids, antelopes, rodents and marsupials--in fact, probably in most animals--the rates of energy and water turnover are linked to salt tolerance, renal concentration and protein synthesis rates. Evolution in wet areas is associated with high turnover rates and low salt tolerance, while desert derivation goes with low rate functions and high salt tolerance. This basic ecophysiology changes slowly, and animals that migrate to different environments may retain ancient patterns in areas where they seem inappropriate--so that cattle keep their high rates of energy and water use in arid zones, or llamas remain low in energy and water turnover after three million years in cool or wet environments. The rate functions may be linked through gene-controlled rates of protein synthesis and turnover, which evolved to run at high rates in well-supplied areas, and at low rates in the face of the sparse resources of the desert.

Animals

Genomics and social practices at Mogou and other Gansu sites during prehistoric trans-Eurasian exchange.

Beginning approximately 4,000 years ago, southwest-Asian-originating domesticated crops and livestock began appearing in Gansu, a key crossroads in northwestern China, yet the population dynamics and social practices underlying these historically transformative events in the region have not been fully explored. Despite the adoption of western domesticates, genome sequences of 149 individuals from the large Mogou cemetery and ten other sites in Gansu, dating between 4,700 and 3,000 years ago, revealed migrations within East Asian regions but no detectable evidence of genetic influence from western or central Eurasia, suggesting that early agricultural dispersals may have followed a model distinct from that documented in Europe and Central Asia. The Mogou cemetery represents a continuous community that interacted with surrounding regions but does not exhibit clear matrilocal or patrilocal residential patterns. We found no strong evidence that co-buried individuals represented biological relatives. Non-local ancestry appears to be linked to lower-status burial practices.

Humans

Studies of ancient crania from northern Africa.

Historical sources and archaeological data predict significant population variability in mid-Holocene northern Africa. Multivariate analyses of crania demonstrate wide variation but also suggest an indigenous craniometric pattern common to both late dynastic northern Egypt and the coastal Maghreb region. Both tropical African and European metric phenotypes, as well intermediate patterns, are found in mid-Holocene Maghreb sites. Early southern predynastic Egyptian crania show tropical African affinities, displaying craniometric trends that differ notably from the coastal northern African pattern. The various craniofacial patterns discernible in northern Africa are attributable to the agents of microevolution and migration.

Africa, Northern

What Uniparental Lineages Tell Us About the Prehistoric Human Colonization of the Americas.

OBJECTIVES: From the perspective of uniparental markers, the view of the human prehistoric settlement of America is that it resulted from a single main migration after the Last Glacial Maximum, following a long or short period of genetic isolation in Beringia. Ancient DNA and whole genome analyses have confirmed this view. My objective here is to demonstrate that humans entered America before the LGM and that the documented post-LGM expansions began in South instead of North America. METHODS: In this work, I have reanalyzed all publicly available mitochondrial DNA and Y-chromosome haplogroups in the American population using simple phylogenetic and phylogeographic methodologies. RESULTS: The arrival of the American settlers occurred more than 30,000 years ago, preceding the LGM. As genomic studies have uncovered, at least two Asian populations contributed to the ancestry of the immigrant population. Low population density and climatic deterioration led to a long period of demographic eclipse, during which small bands of hunter-gatherers made long journeys in search of favorable niches. After the LGM, the climate improved, and demographic expansions occurred in multiple independent centers. The founding and expansion ages of the uniparental haplogroups indicate that these centers were in South America, particularly the Colombian isthmus, the Andean region, the Southern Cone, and the Amazon. Subsequent dispersals occurred in North America, one involving mitochondrial haplogroups A2, C1, and D1, but not B2, and another, of lesser magnitude, represented by the expansion of haplogroups C4c and X2a. CONCLUSION: This work offers a previously unexplored model for the colonization of the Americas.

Native American

Tooth movement.

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Bone and Bones

Evaluating residence patterns among prehistoric populations: clues from dental enamel composition.

We determined enamel composition (Ca, P, Mg, Cu, Mn, Se, Zn, Al, Sr, Pb) for the mandibular canines of 94 individuals from 4 prehistoric Arikara cemetery populations, collecting the compositional data using scanning electron microscopy energy dispersive x-ray analysis. We examined each of the four samples independently and then pooled them for a group comparison using correspondence analysis. The results indicate significant intrapopulational dispersal, particularly when viewed by age and sex subgroups. When all sites are included for correspondence analysis, a distinctive pattern of adult male dispersal compared to the more tightly clustered adult female and subadult subsample is apparent. We hypothesize that the observed pattern of dispersal indicates local geographic and possible dietary differences among the groups. Furthermore, we hypothesize that the observed differences between males, and females and subadults for each site are the result of a residence pattern of out-migration for males.

Dental Enamel

The Jewish contribution to medicine. Part I. Biblical and Talmudic times to the end of the 18th century.

Jewish interest in medicine has a religious motivation with the preservation of health and life as religious commandments in the Holy Scriptures. Despite a basic belief that God caused disease and effected cures with physicians as agents, Jews accepted the rational medicine of ancient Greece. They assisted in the spread of these teachings in the Roman and Arab empires but carried them to the rest of Europe in their migrations. Jews were able to bridge the educational gap of a 500-year period of exclusion from universities and medical schools in the Middle Ages through the Talmud, which started as a commentary on the scriptures in the 5th century BC, but developed over the centuries into a comprehensive body of learning incorporating law, art and the sciences.

History, 15th Century

[Diversity of malaria in the Sahelo-Saharan region. A review apropos of the status in Niger, West Africa].

The concept of epidemiologic facies of malaria underlines the diversity in the expression of the disease in areas where important ecological variations interfere largely with transmission. Niger is quite a border region between the afrotropical fauna from the south and the Palearctic fauna from the north. The last one filters through the mountains where it maybe represents a relic of ancient paleoclimates. Annual variations of the northern limit of Anopheles arabiensis, in the Sahelo-Saharan region including some oasis, are related to temporary breeding places produced by seasonal rainfall, after estivation during the dry season or after a long migration with the wind. An. gambiae s.s is present in the south and along the Niger river, with An. funestus, even till Zinder. The northern limit of An. nili is the Niger river. The permanent variations of the environment induce great differences in the level of transmission between an intermediate stable situation in the south to an unstable one in the north. Epidemic outbreaks appear some years in vulnerable populations. The implementation of a malaria program supposes to take account of the various eco-epidemiologic situations all over the country. Even if mortality and morbidity became lower, natural precaution in some groups of people must be preserved.

Adolescent

[Hippocratic concept of hysteria].

The Greek physicians of the fourth century B.C. painstakingly described a number of symptoms that they thought were caused by migrations of a restless uterus, said "wandering womb". According to this concept, we can use the term "hysteria", despite the fact that the noun itself never appears in any of the Hippocratic texts. We can determine its origin as being in ancient Egypt from the medical writings of the Egyptian papyri. In the same way, the therapy is mainly of Egyptian origin, using a combination of recipes to make the moving womb return to its proper place in the body cavity. However, we can also identify the rationality of the Greeks, in particular as regards mechanical physiopathology. Hippocratic authors are closely connected with presocratical physics, and manifest a distinct break with magic and religion. Furthermore, they claim that hysteria may result from prolonged sexual continence, an opinion which was to influence medical history for over two thousand years.

Egypt, Ancient

Local ancestry inference identifies robust evidence of selection in Neolithic Europe.

During the European Neolithic, migrating Anatolian farmers admixed with local hunter-gatherers, coinciding with major shifts in diet, environment, and lifestyle that imposed strong selective pressures. Local ancestry inference is widely used to detect selection following admixture, but most methods were developed and validated on present-day populations. Their performance in ancient DNA - where reference panels are smaller, data are sparser, and admixture is more ancient - remains unresolved. We benchmark eight local ancestry inference methods on 176 imputed Neolithic genomes. While individual-level ancestry estimates are highly correlated across methods, inferred tract lengths and admixture time estimates vary by an order of magnitude. Overall, we recommend Gnomix or RFMix for general use. We also investigated our ability to detect natural selection using LAI. Integrating results across methods and replicating across methods and in two independent datasets (n=378 and 1,121) we identify a robust ancestry deviation at FADS1/2, consistent with adaptation on metabolism. We also identify IRAK4 (innate immunity) as a candidate locus, but with less consistent signal across methods. Finally, we replicate previous reports of excess hunter-gatherer ancestry at the HLA, but these results are inconsistent across methods and suggest that they may be affected by bias in local ancestry inference. Our findings demonstrate that while local ancestry inference recovers biologically meaningful signals in ancient genomes, results can be sensitive to the methods used for inference, particularly in complex regions like the HLA. Method choice critically influences inferred ancestry patterns and selection signals, underscoring the importance of multi-method validation.

Journal Article