Selective sweep on human amylase genes postdates the split with Neanderthals

Inchley, Charlotte; Larbey, Cynthia; Shwan, Nzar A. A.; Pagani, Luca; Saag, Lauri; Antão, Tiago; Jacobs, Guy S.; Hudjashov, Georgi; Metspalu, Ene; Mitt, Mario; Eichstaedt, Christina A.; Malyarchuk, B. A.; Derenko, Miroslava; Wee, Joseph; Abdullah, Sarini; Ricaut, François‐Xavier; Mormina, Maru; Mägi, Reedik; Villems, Richard; Metspalu, Mait; Jones, Martin K.; Armour, John A.L.; Kivisild, Toomas

doi:10.1038/srep37198

Cited by 78 publications

(89 citation statements)

References 36 publications

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“…If an (AMY1) 3 allele was the common ancestral structure for all modern humans, the initial amplification to higher gene copy number may have been selectively advantageous before the neolithic, consistent with a recent analysis of sequence data [Inchley et al, 2016]. Nevertheless, whether adaptive or neutral, a preneolithic expansion to higher copy number does not itself preclude subsequent adaptive value for copy number change after the neolithic [Perry et al, 2007].…”

Section: Discussionsupporting

confidence: 76%

Recurrent Rearrangements of Human Amylase Genes Create Multiple Independent CNV Series

et al. 2017

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19The human amylase gene cluster includes the human salivary (AMY1, MIM# 20 104700) and pancreatic amylase genes (AMY2A, MIM# 104650 and AMY2B, MIM# 21 104660), and is a highly variable and dynamic region of the genome. Copy number 22 variation of AMY1 has been implicated in human dietary adaptation, and in 23 population association with obesity, but neither of these findings has been 24 independently replicated. Despite these functional implications, the structural 25 genomic basis of copy number variation (CNV) has only been defined in detail very 26 recently. In this work we use high-resolution analysis of copy number, and analysis 27 of segregation in trios, to define new, independent allelic series of amylase CNVs in 28 sub-Saharan Africans, including a series of higher-order expansions of a unit 29 consisting of one copy each of AMY1, AMY2A and AMY2B. We use fibre-FISH 30 (fluorescence in situ hybridization) to define unexpected complexity in the 31 accompanying rearrangements. These findings demonstrate recurrent involvement 32 of the amylase gene region in genomic instability, involving at least five independent 33 rearrangements of the pancreatic amylase genes (AMY2A and AMY2B). Structural 34 features shared by fundamentally distinct lineages strongly suggest that the common 35 ancestral state for the human amylase cluster contained more than one, and 36 probably three, copies of AMY1.

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Section: Discussionsupporting

confidence: 76%

Recurrent Rearrangements of Human Amylase Genes Create Multiple Independent CNV Series

et al. 2017

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“…After being exposed to saliva for 60 minutes (Figure 3H) the boiled starch granules were degrading. The results of this simple experiment are consistent with many studies which have shown that amylases are much more active on starch granules that are partially gelatinised than they are on intact starch granules 72,[74][75][76] . and linolenic), potentially from pine nuts.…”

Section: Foodsupporting

confidence: 90%

“…All higher primates have AMY1 ; however, the number of AMY1 genes duplicated at some point in the hominin lineage, which increased the efficiency of starch digestion due to greater capacity for amylase action. The timing of the duplications of the AMY1 gene in humans is unclear; it may have occurred after the modern human line branched off from the Neanderthals and Denisovans, although higher AMY1 copy numbers have also been detected in a pre‐Neanderthal ancestor . On exposure to saliva, even starch granules that have been only partially disrupted by cooking would be very susceptible to breakdown and very unlikely to survive to become embedded in dental calculus (Figure ).…”

Section: Categories Of Materials Recovered From Dental Calculusmentioning

confidence: 99%

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes

Hardy

Buckley

Copeland

2018

Evolutionary Anthropology

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Dental calculus is now widely used to recover information on items ingested in the past. It is particularly valuable in the earlier Paleolithic, where recovered data may represent the only evidence for plant use. Several recovery methods are used and each one produces different results. Biomolecular markers and genetic material recovered from dental calculus is providing new data on identifiable dietary and medicinal items and human microbial communities. The recovery of microfossils, in particular, starch granules, has triggered a new awareness of the role of plants in the diet throughout the Paleolithic. However, the minute amount of material recovered has little relationship with food eaten during a person's life, while salivary amylase breaks down cooked starch. Therefore, broader dietary interpretations and detection of cooked food are problematic. The study of ancient dental calculus holds great potential to recover information about past lives, within realistic parameters.

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“…Time to the Most Recent Common Ancestor (TMRCA) were also calculated for 10kbp sequences (Inchley et al 2016) surrounding each insertion site ( Supplemental Table S10, details in METHODS). Of the 24 insertions that are fixed or almost fixed in al modern populations, we selected those showing a TMRCA compatible with the split between AMH and HN/HD (TMRCA < 800 Kya) as potential candidates for selection/spread along the AMH lineage.…”

Section: Amh-specific Ris In Present-day Populationsmentioning

confidence: 99%

“…The time to the Most Recent Common Ancestor (TMRCA) of each 10kbp regions encompassing a given insertion was estimated as described elsewhere (Inchley et al 2016) based on 1000 Genomes sequences of AFR samples to avoid potential backwards biases due to the documented Neanderthal introgression in 28 Eurasians . All AFR individuals, and not only carriers of an insertion, were used for this calculations.…”

Section: Tmrca Estimates Of Genetic Regions Surrounding Amh-specific Rimentioning

confidence: 99%

Impact of non-LTR retrotransposons in the differentiation and evolution of Anatomically Modern Humans

Guichard

Peona

Malagoli-Tagliazucchi

et al. 2017

Preprint

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Transposable Elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) extensively shaped the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. Briefly, we first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. Notably, these insertions targeted genes more frequently than randomly expected and are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes targeted by human-specific N-LTRr insertions seems to reflect phenotypic changes that occurred during human evolution. Furthermore, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we also identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, which show traces of positive selection and are now fixed in all present-day human populations. In sum, our results strongly suggest that N-LTRr impacted our differentiation as a species and have been a constant source of genomic variability all throughout the evolution of the human lineage.

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Selective sweep on human amylase genes postdates the split with Neanderthals

Cited by 78 publications

References 36 publications

Recurrent Rearrangements of Human Amylase Genes Create Multiple Independent CNV Series

Recurrent Rearrangements of Human Amylase Genes Create Multiple Independent CNV Series

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes

Impact of non-LTR retrotransposons in the differentiation and evolution of Anatomically Modern Humans

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