Genetics Trumps History?

The history books in school usually teach about the decline of indigenous American populations due to exploration, conquest, and massacre at the hand of European explorers. Though the Zapotec civilization had already mostly disappeared by the time the Europeans arrived in Mexico, historians had still attributed its people's near-complete disappearance to European activity. However, a recent mtDNA study shows that significant population decline occurred well before first European contact, suggesting that other factors were at play in gene flow decline.

This can, perhaps, be applied as an mtDNA study of more indigenous populations, so as to see the effects of contact with European populations more closely.

Source: Here

The British Are Coming!

A team of researchers (Schiffels et al, 2015) from the United Kingdom, Germany, and Australia has released a pre-publication report of ten complete genomes retrieved from Iron Age and Anglo-Saxon (2,300-1,200 years before present) individuals from East England, near Cambridge. This ancient DNA was compared to modern samples, to the conclusion that modern English are genetically more similar to the older Iron Age humans than to the Anglo-Saxons. The Iron Age samples showed closest affinity to modern English and French people, while the Anglo-Saxons were closer to present-day Scottish and Norwegians. Furthermore, Schiffels et al conclude that the ancient Anglo-Saxon individuals were most similar to the modern Dutch and Danish, and contributed roughly 30% to the genome of modern East English; on the other hand, the Iron Age individuals share more recent common ancestry with more ethnic groups from across Northern Europe, including England.

Fig. 1 (Schiffels et al 2015)

Perhaps most interesting are the interpretations yielded by the in situ burial sites. The ancient community at Oakington, one of the sites excavated, is described as "genetically mixed but culturally Anglo-Saxon," opposing the expectation that interactions between indigenous and immigrant peoples would result in total segregation. Of the genome-sequenced individuals buried at Oakington, two appear to be recent immigrants from different European sources, one appeared descended from the native Iron Age population, and one exhibited admixture from both indigenous Iron Age and immigrant genomes; all four were buried similarly, however, in a flexed position with grave goods. Schiffels et al note that the only grave without any burial possessions belonged to one of the "foreigners," while the grave most abundant with good belong to the "native British." They suggest this signals some kind of socioeconomic disparity between old-timers and newcomers on the ancient British Isles---an interesting if perhaps nebulous claim, nonetheless representative of a fascinating find in the intersecting realms of archaeology and ancient genomics.

Fig. 2 - Schiffels et al (2015)

Erin Go Bragh?

PhD student Harriet Donnelly, from the Department of Archaeology at the University of Sydney, Australia, recently published this interesting review of the genetic and archaeological evidence for defining "the Celtic people" as a distinct Iron Age ethnic group. In this piece, Donnelly proposes that the ancient Celts were in fact not their own ethnic group, based on archaeological as well as genetic evidence.

Traditionally, "the Celts" are referred to as the tribal peoples inhabiting Europe from the British Isles all the way to the Iberian Peninsula in the west and Anatolia in the east; the ancient Celts lived from Iron Age well into the Roman Age, during which time their homelands became the Roman provinces of Celtiberia, Brittania, Pannonia, Gallia, and Galicia. The Celts who remained in Britannia are known as the Insular Celts, whose descendants the Gaels (from an Old Welsh word possibly meaning "forest people") populated Ireland, Scotland, and the Isle of Mann. The modern idea of "Celtic identity," however, as exemplified by popular culture and the six member "Celtic nations" recognised by the Celtic League (Brittany, Cornwall, Isle of Mann, Ireland, Scotland, and Wales), is largely the product of a 19th-century revivalist movement, promoting Celtic nationalism in Ireland especially against modernisation by British overlords. Into the 1920s this so-called Celtic Revival further led to interpretations of the Irish people as a separate "race" from other Europeans, suggested by their evidently ancient divergence---cultural, linguistic, and presumably genetic---from the rest of the continent.

Yet Donnelly presents in her article that mitochondrial DNA implies incredibly close relatedness between modern "Insular Celts" and other Europeans from across the central continent, with settlement of the British Isles by these maternal ancestors falling in the late Neolithic and Early Bronze Age; by contrast, Y-chromosomal DNA appears to show closer relatedness among modern peoples along the Atlantic coast, with contributions from Iberian males entering the British Insular genome by the end of the Bronze Age at the latest. Donnelly argues that this means the ethnic groups present in the Celtic Nations from the Iron Age through the Roman Era cannot be called a genetically distinct group. Furthermore, archaeological materials such as fibulae (e.g. decorative pins, brooches), swords, Greek amphorae, and dragon motifs of great similarity are consistently found all across the formerly "Celtic" realm; Donnelly interprets this to represent a great deal of trade and exchange of ideas through the Iron Age, but not necessarily "the expansion of a 'people.'" So the idea of an ancient "Celtic culture" suddenly rising up, fanning out, and taking hold in Europe may not in fact hold. Rather, the Iron Age of Europe seems to be characterised by a vast network of trade routes connecting a wide region, occupied by people who were not so different from one another.

Fig. 1 - Asterix the Gaul & friends --- Celts, or not?

Adaptive Introgression

There have been many studies on variations in the human genome. As a species, we are generally curious as to our origin and how quickly adaptive traits such as skin pigmentation can occur in a population and how adaptive traits could have developed. It appears that there was admixture to some extent in human populations between African populations and Eurasian populations, as well as some gene flow between Eurasian humans and Neanderthals. The study touches on admixture between modern and archaic humans addresses the possible the adaptive advantages of Neanderthal and Desnovian populations mixing with archaic humans and to what extent hybridisation occurred. It is now generally accepted that Neanderthal and Desnovian DNA is present in non-African humans. It was believed to have occurred around 60mya which "largely post-dates the African–Eurasian population split, which is estimated to have occurred 100–160 kya (under the slow mutation rate) or 50–80 kya (under the fast rate)." The study focuses on to what extent introgression occurred and what potentially negative or beneficial adaptive outcomes occurred as a result.

Some More Info on Haplotypes

By Alan Templeton, this article is mostly theoretical in its discussion about haplotypes, covering coalescent theory, which traces gene recombination in reverse to determine the generation of the haplotype's first appearance, and phylogeography, which connects the haplotype to the geography in which it originated and the evolutionary factors contributing to a gene's high distribution, The read is fairly dense, but may provide additional insight (or confusion!) regarding the Reich et al. 2012 and Chatters et al. 2014 that address the peopling of the Americas.

Sedimentary Ancien DNA and the Mesolithic-Neolithic transition

An article published earlier this year in the journal Science described a new discovery that changed the archeological community's perception of the Mesolithic-Neolithic transition in Britain. Sedimentary Ancient DNA (sedaDNA) analyses of marine sediment cores revealed traces of wheat dating to 8000 year BP. Wheat is a domesticated plant typically associated with the Neolithic revolution. This finding is surprising, considering that archeological evidence suggests that the Neolithic started on the contient around 7500 BP. The authors suggest that the presence of wheat in Britain could be the result of commercial exchanges with the people of South-Eastern Europe, suggesting more complex networks than previously thought.

The Neolithic revolution is similarly associated with the domestication of animals

Neolithic-Bronze Age Population Dynamics & Cultural Effects in Eurasia

In June, two studies published in Nature revealed the complexities of ancient Eurasian population genomics and the cultural impacts of population migrations. Both studies found evidence that one group of nomads--the Yamnaya steppe herders--entered Europe around the Late Neolithic/Early Bronze Age, likely bringing with them Proto-Indo-European language. One study found these nomads also brought a light skin variant into Europe, but not lactose tolerance. These researchers suggest that the Yamnaya also spread eastward, into the Altai mountains. These results confirm the cultural similarities (particularly their burial practices and pottery styles) archaeologists have noticed between the Yamnaya and the Bronze Age peoples in the eastern Eurasia. 

Article links: here, and here. 

Conservation Laws of Hybrid Species

Hybrid species are relatively rare in nature and are often perceived with some negative connotations due to the implications they are unnatural. Hybridisation, however, occurs quite frequently in nature and, especially with the current global decline of diversity, it is essential to keep these hybrids protected in order to maintain a large variety of species in nature. The article presents the increasing necessity to make defined laws protecting the species in order to keep the diversity for gene flow between species relevant, and emphasises the differing perceptions on genetic hybridisation based on the familiarity with individual species; mammals having generally negative connotations, where amphibians or reptiles are generally more neutral. The most important aspect of the protection of the species is to maintain biodiversity and allow for adaptations to occur without human interference in the species prevalence.

Oldie But Goodie

Using autosomal internecine non repetitive sequences from the human genome, researchers were able to estimate divergence times on the molecular clock for humans and chimpanzees, and the point at which gorillas broke off from their shared branch. In retrospect, this study now confirms the current working model, in addition to confirming that humans and chimps have about a 1% DNA difference. However, using tree parsimony based on independent analysis of 22 of the 53 segments, the researchers also estimated the effective population of the Pan/Homo common ancestor to be larger than previously thought. By analyzing the 53 segments in combination with 37 protein genes, researchers estimated that this effective population was somewhere between 52,000 and 96,000 individuals, as opposed to the 10,000 that had previously been suggested. Given this, the researchers conclude that the effective populations of Homo experienced a drastic reduction post-Pan split.

Source: Am. J. Human Gen. (2001)

Adaptive Radiation & Species Richness - Speciation at "Bat"

Bats represent one of the most intriguing mammals on Earth; they are a case study in the convergent evolution of flight among multiple extant clades, as well as, according to this new study, a fascinating example of adaptive radiation and prolific speciation. The article from Shi & Rabosky, published in Evolution this year, notes that bats are the second-most species-rich group of mammals alive today, with more than 1,300 distinct species alive today. By alignment of mitochondrial and nuclear sequences, and calibration to known fossil bats, the research team constructed the phylogeny below of 812 living bat species.

Fig. 1 - Phylogeny of 812 bats, with timescale (Fig. 2 in Shi & Rabosky 2015)

The phylogeny shows speciation of the 6 major families of bats during the Eocene, around 40-55 Ma. The researchers report a homogeneous, even "explosive" diversification of most bats, with clades that radiated longer ago being more diverse today, but with an overall trend to decreased rate of speciation from the late Eocene into the present; one subfamily, however, the stenodermatines, defies the slower-speciation trend. This subfamily is characterised by relatively recent cranial adaptation for eating hard fruits; Shi & Rabosky suggest this venturing of a bat subfamily into a new niche could explain the radiation into such species richness within the hard-fruit-eating clade. As with all phylogenies, and especially those calibrated to an incomplete and ever-expanding fossil record, there is the risk that some species represented in the tree above are calibrated to incorrectly assigned fossils. Nonetheless, the fact remains that since an ancient mammal developed the ability to fly and entered the sky, thus entering into a previously mammal-free niche, bats have done extraordinarily well, adapting to an incredible number of ecosystems and habitats all over the world.

Fig. 2 - See? Bats are really really diverse.

Darwins Finches, introgression, and adaptation

The finches of the Galapagos Islands have been the focus of continued interest since Darwin fist studied them. This long term interest on the 14 species that comprise Darwin's Finches has continued to produced a wealth of research in both the fields of biology and ecology. Genetics is also providing a new wealth of knowledge the developement and gene flow between Darwin's Finches. This article reviews the ways in which genetics has been integrated with field biology to discuss the genetic basis for some of the topics field researchers are showing. On interesting study demonstrated how the gene Bmp4 influences the morphological development of the beak. The morhpological differences in the beak have often been linked with differences in vocalization which may promote reproductive isolate.  Beak developement is not the only thing discussed. The article also discusses the integration of gemonics in order to understand adaptive radiations, and the subsequent gene flow between the different populations.

Hadza Tuber Digestibility and the TIM-1

An interesting study conducted by Schnorr et al. 2015, the researchers looked into the digestibility of underground storage organs (USOs, wild plant foods like Hadza tubers) through the use of a "dynamic in-vitro gastro-intestinal model", TIM-1. These foods are known to be toxic when raw and have indigestible husks, requiring food processing to be edible and provide metabolic benefits for Hadza hunter-gatherers; TIM-1 supposedly recreated the functioning of an actual GI tract, allowing the researchers to measure tuber digestibility and assess nutritional value.

While the study found that tubers were rich in minerals like calcium, iron, potassium, and magnesium, absorption in the TIM-1 was low and varied, which the researchers attributed to variation in the species of tuber collected for testing. The TIM-1 was also found to be problematic in the absence of the inclusion of microbiota and independent metabolic rates, which would also affect food consumption.

Environmental change, genetics and speciation

Environmental change is among the key factors that is thought to have highly affected the evolutionary course of many lineages by causing speciation, extinction and species turnover. A recent publication on PLOSone about Chacma baboons from South Africa shows that the geographic structure and demography inferred from mtDNA matches what’s expected from phylogentic and climatic studies indicating that changing climatic condition in the Pleistocene had indeed affected the demography and distribution of the species. The study reports that two marker regions in the mtDNA derived from fecal samples show the Chacma baboons diverged into two distinct mitochondrial clades around 1.9-1.6Ma, a time period, which coincides with a major shift to aridity.

Cleaning the Ancients

Ancient DNA is notoriously easy to contaminate, requiring special protocols in all steps of its purification and identification process. Even when taking proper contamination precautions, sequencing of aDNA is hard due to poor preservation. However, a new protocol has shown some promise for increasing endogenous DNA extraction. By 'pre-digesting' bone and tooth fragments, endogenous DNA yields can be increased by nearly 300%, which will allow us to make new discoveries.

Source:
http://www.nature.com/articles/srep11184

Reading Between the Lines: Analysing Ancient DNA from Parchment

Prior to the widespread production of paper, parchment produced from animal skins was the preferred medium of Western cultures for the inscription of important messages and correspondence. There is undeniable value in the words of the past preserved on such parchments, as they can tell us about the history of language, law, society, and culture. One aspect of culture most fascinating to elucidate is the origin story of human agriculture and livestock production. Now, a team of researchers reports that such information can be reaped from these ancient documentary treasure troves---not just from the words written on them, but from the parchments themselves.

As ancient and medieval parchments are made from animal skins, they represent, in the words of the researchers, a "reservoir of ancient DNA." In their study of two Northern English documents from the 1600s and 1700s, they found that the skins used for printing had been from a sheep; this gives evidence to the raising and farming of sheep in this geographic region at that point in history, evidence which stands to augment and uphold (or refute/negate, in future studies of parchments from elsewhere) previously understood hypotheses about livestock culture. Naturally, more precious and rarer scrolls from elsewhere in the world may be harder to pry from the hands of their curators for mining of ancient DNA. However, with the promise of elucidating the deep origins of humans' non-consumptive use for different animals--as well as using genetics to map the migration and spread of domestic livestock among vast regions--this technique might be worth reading between the lines for.

Can Man's Best Friend Help Us Understand Human Evolution and Disease?

Dog's have long been known as man's best friend. However, just how long have these loyal companions been companions of our ancestors? In the article on Nature, it is believed that the oldest link between the domesticated dog and the grey wolf is the Chinese indigenous dog. Based on the genome sequence of four grey wolves, three Chinese dogs, and three modern breeds, the study demonstrated Chinese indigenous dogs being the closest link to both wolves and dogs. The spilt is believed to have happened around ~32,000 years ago. The paper touches on the estimated time elapsed since the divergence of the populations, and even touches on the genes identified to regulate certain traits. By recognising the parallelism evolution of grey wolves into the modern dog, it may be possible to better understand and analyse the genes in digestion and metabolism, neurological processes, and perhaps even cancer.

Good losses?

What makes humans unique is a question that is raised very often. A study that looked at sequences that are highly conserved in chimpanzees, our closest relatives, has revealed that there are 510 deletions of non-coding regions in humans that are mainly related to hormone signaling and neural functions. Transgenic analysis of a chimpanzee and a mouse to explore the function and expression of deleted elements show that these deletions appear to correlate with both loses and gains of traits that are unique to humans and also might have played an important role in the evolution of Anatomically Modern Humans. Examples mentioned include losses that led to tissue expansion, such as expansion of the cerebral cortex and loss of penile spines. The study also reports that of these deletions 88% are reported missing from the Neanderthal genome.

Gene, Pots, and the Origins of the Indo-European Language Family

Archaeologists have featured heavily in a long-standing debate regarding the origins of the Indo-European language family. Currently the debate focuses on two main hypotheses. The first suggests that Proto-Indo-European people spread out of Anatolia during the Early Neolithic. On the other hand, others have argued that these people expanded later in time, during the Copper Age and early Bronze Age from the Pontic-Casbian steppe. To shed light on this issue, two independent studies amassed samples of aDNA from several cultures across Europe and Central Asia and from 6000 BC to 900 BC. Interestingly, both studies revealed afinities between the corded ware (2500 BC) people of Central Europe and the Yamnaya steppe culture, suggesting a westward expansion. The data also suggest an eastward expansion out of the Pontic-Casbian Steppe into East Asia, as illustrated by genetic afinities between the Yamnaya and the Afanasievo. Though the sample size is still small, the genetic data seem to support the notion that the Proto-Indo-European language may have spread into Europe and Asia during these expansions.

What was most striking is that this topic has been the focus of debate for 200 years! While these studies do not prove the origin of this language family, they do provide a way to assess the likelihood of these proposed scenarios based on the timing and placement of genetically documented expansions.

Link to article

The Effects of Social Organization on mtDNA and nDNA

This study draws on the analysis of a living population to determine the effectiveness of archaic studies driven purely by mtDNA or nDNA, hoping to shed some light on genetic processes that cannot be accounted for on the basis of such things as samples limited in their size, or even through the social processes that influence inheritance. The Yanomamo are an endogamous group in South America that informed the basis of this study.

Ancient DNA sheds light on existence of rare extinct dog

A recent study published in PLOS ONE details the sequencing of ancient mitochondrial DNA from an extinct canid species. Kurīs were small to medium dogs that are believed to have travelled through Oceania alongside Polynesian settlers in the 14th century. Preservation of remains is difficult in the Pacific and thus the archeological record for these ancient dogs is relatively scarce. Greig and colleagues' research showed that modern day Indonesian dogs are close relatives of the kurīs and that the species stemmed  from a small founding population of closely related individuals.

Ancient African genome reveals the complexity of human migration

The analysis of a genome from an ancient Ethiopian specimen was published today in Science. The DNA came from the inner ear bone of an ancient hunter gatherer man nicknamed Mota, who lived about 4,500 years ago in the Ethiopian highlands.

Comparison of 250 bp of his genome with other human sequences reveals that Mota is most similar to individuals of the Ari ethnic group. The sequences where Mota and the Ari differ, however, contain DNA shared with Europeans. This suggests that a large group of Middle Eastern farmers migrated into Africa about 3,000 to 3,500 years ago, where they passed on the DNA that links Europeans with living Africans.

Next-generation sequencing sheds light on bird phylogeny

Portion of the massive phylogeny presented in the paper

A paper published in this week's edition of Nature presents a new phylogeny of Neoaves (most extant birds), based on next-generation sequencing. Using 198 modern birds, the analyses reveal five main sister groups within Neoaves. Some of the groupings contradict findings by another research group who analyzed the genome of 48 bird species and published in Science last year.

The authors claim their results support the paleontological record for these species.

Function & Evolution of a Polymorphic Inversion on Human Chromosome 19

Though chromosomal inversions have been studied for several decades, it has been unclear as to how they are maintained in populations and why they may be selected for. To address these questions, a recent publication in PLoS Genetics explores one particular inversion in humans, a 415 kb inversion on chromosome 19. Via comparison of the genotypes of 541 individuals, the researchers found that this inversion is polymorphic in humans, and is mainly found in East Asian populations at a frequency of 4.7%. They estimate that this inversion originated about 50 to 40 ka and its effects are possibly deleterious.

Food Industry Revolution

Here's a recent article relevant to our GMO discussion a couple weeks ago.