Expansion of modern humans over the world: The origin when considering non-linearity

Cenac, Zarus

doi:10.1101/2023.03.11.532168

Cited by 4 publications

(18 citation statements)

References 28 publications

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“…Relationships between distance from Africa and diversity appear to be better shown through quadratic (than linear) trends for autosomal microsatellite heterozygosity and also mitochondrial diversity, but this is not apparent for autosomal SNP haplotype heterozygosity, X-chromosomal microsatellite heterozygosity (Cenac, 2023) and Y-chromosomal haplotype diversity (present study). Therefore, r s were used for rankings regarding autosomal SNP haplotype heterozygosity, X-chromosomal microsatellite heterozygosity, and Y-chromosomal haplotype diversity, whilst R 2 s were utilised for rankings concerning autosomal microsatellite heterozygosity and mitochondrial diversity.…”

Section: Methodscontrasting

confidence: 62%

“…To find the ranks, correlation coefficients (rs) or R 2 s were worked out concerning each variable and distances from the 99 Betti et al (2013) African origins (through the use of distances from Cenac, 2022Cenac, , 2023, who used the Betti et al origins, or distances found in the current study which used those origins toosee Method: Geographical distance). Between autosomal microsatellite and autosomal SNP haplotype heterozygosities, ranks were averaged at each origin.…”

Section: Estimating the Origin Across Variablesmentioning

confidence: 99%

“…Preprints have concerned non-linearity (Cenac, 2022(Cenac, , 2023. Unlike autosomal SNP 3 haplotype heterozygosity, X-chromosomal microsatellite heterozygosity, and cranial shape diversity, both autosomal microsatellite heterozygosity and mitochondrial diversity may be better described as having quadratic relationships with distance from Africa rather than linear declines (although support for a quadratic relationship regarding mitochondrial diversity could arise from climate) (Cenac, 2023). And so, there could be a point in considering non-linearity with respect to distance (e.g., from Africa) and Ychromosome-derived haplotype or repeat unit diversities, TMRCA, effective population size, and expansion time.…”

Section: Non-linearitymentioning

confidence: 99%

“… In Tishkoff et al (2009), the waypoint is for expansion from Africa to Asia (Asia clearly being right next to Africa in maps inTishkoff et al, 2009).7 To calculate r correlation coefficients and R 2 s, distances calculated inCenac (2022Cenac ( , 2023 were used apart from with respect to Y-chromosomal haplotype diversity.8 From peak points for each of three types of autosomal diversity, Cenac (2022) calculated a centroid as an overall…”

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confidence: 99%

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Y-chromosomal microsatellites and expansion from Africa

Cenac

2023

Preprint

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Some diversities are thought to mark human expansion from Africa — they decline as distance from Africa accumulates, and suggest that the expansion originated from any of a range of locations which are only in Africa. Previously, a decline was found regarding Y-chromosomal microsatellite heterozygosity. However, this diversity has been noted to suggest a non-African starting point and, consequently, not appearing reflective of expansion from Africa. Declines have appeared in other variables derived through Y-chromosomal microsatellites, including effective population size, expansion time, and time to the most recent common ancestor. The present research inferred if these variables, and some Y-chromosomal diversities, indicate expansion from Africa; indicative variables could help with identifying which area of Africa the expansion started in. This research used variables derived previously from Y-chromosomal microsatellites for populations worldwide (effective population size, expansion time, and time to the most recent common ancestor) or only in Africa (haplotype and repeat unit diversities). Regarding populations worldwide, San were very high in each variable when considering distance from (southern) Africa. Without San, effective population size and time to the most recent common ancestor did not squarely indicate an African origin, and expansion time placed the origin wholly outside of Africa. When using San, each area was only in Africa. Amongst African populations, whilst both haplotype diversity and repeat unit diversity showed a geographical pattern of declining, only haplotype diversity suggested a completely African area of origin. Using Y-chromosomal haplotype diversity alongside some other genetic diversities, a southern African origin was broadly indicated.

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Section: Methodscontrasting

confidence: 62%

Section: Estimating the Origin Across Variablesmentioning

confidence: 99%

Section: Non-linearitymentioning

confidence: 99%

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Y-chromosomal microsatellites and expansion from Africa

Cenac

2023

Preprint

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“…The location where the decline is at its most negative can be called the peak point (e.g., Cenac, 2022). Like has been done with correlation coefficients for relationships between genetic diversity and distance from Africa (Luca et al, 2011; Ramachandran et al, 2005), Figure 1 presents correlation coefficients ( r – blue areas) regarding X-chromosomal microsatellite heterozygosity and distance from Africa (coefficients are from Cenac, 2023a, who used diversities from Balloux et al, 2009, and distances in Cenac, 2022). The peak point is the location giving the lowermost correlation coefficient (Cenac, 2022) (green circle).…”

Section: Introductionmentioning

confidence: 99%

X-chromosomal diversity may reflect climate (when considering human expansion from Africa)

Cenac

2023

Preprint

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A decreasing of diversity with increasing distance from Africa has been interpreted as a signal of modern humans having expanded (across the globe) from Africa. Research is consistent with a climatic signal being present in mitochondrial diversity, but not in other genetic diversities (e.g., X-chromosomal) or cranial diversity. Some of that research involved adjusting diversity for distance from Africa, and seeing whether this adjusted diversity is associated with climate. The choice of African location which the distance from Africa is measured from may affect whether adjusted diversity appears to be related to climate. To bypass this potential effect of location, some analyses in the present study featured only populations outside of Africa. Other analyses included African populations. The present study used diversities, distances, and minimum temperatures from beforehand. Autosomal, X-chromosomal, and cranial diversities were adjusted for distance from Africa. Y-chromosomal diversity was adjusted for distance from Asia because previous research suggested that Y-chromosomal microsatellite heterozygosity offers more support to expansion from Asia (than Africa). Whether populations were worldwide or only outside of Africa, adjusted X-chromosomal diversity increased with minimum temperature. Other adjusted diversities were not related to minimum temperature. Perhaps previous research found no indication of a climatic signal in X-chromosomal diversity because of two populations, one of which likely had an atypical adjusted diversity for their minimum temperature. These populations may have led to heteroscedasticity and the climatic signal being obscured.

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Cranial sexual dimorphism levels in modern humans: Supporting a global expansion originating in southern Africa

Cenac

2024

Preprint

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Modern humans are acknowledged to have expanded across Earth from Africa. Biological measures have appeared to reflect this expansion, such as genetic diversity and cranial sexual size dimorphism. Admixture is known to be an issue for using diversity to locate where the expansion set out from in Africa; using cranial dimorphism should make admixture less of an issue. Therefore, cranial dimorphism could be of importance for clarifying the origin. This study used data sourced from the Howells dataset to infer if cranial form and shape dimorphisms indicate the expansion, and understand why cranial size dimorphism looks indicative. Form and shape dimorphisms were calculated through RMET. Size dimorphism was calculated beforehand. Cranial form and shape dimorphisms increased with distance from Africa. Form dimorphism suggested an area of origin which was predominantly in Africa and marginally in Asia. For shape dimorphism, locations spanned much farther beyond Africa. Hence, cranial form dimorphism seemed to be quite indicative of the expansion, unlike cranial shape dimorphism. Form is known to feature size and shape – cranial form dimorphism may signify the expansion mainly, or only, due to cranial size dimorphism. It seemed unsettled why cranial size and form dimorphisms seem related to the expansion because it was vague whether cranial size indicates the expansion more for males than females. Previously, a collective estimate of the origin (from biological measures including cranial size dimorphism) pointed to southern Africa; in the collective estimation process, cranial size dimorphism supported the south as would cranial form and shape dimorphisms.

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Expansion of modern humans over the world: The origin when considering non-linearity

Cited by 4 publications

References 28 publications

Y-chromosomal microsatellites and expansion from Africa

Y-chromosomal microsatellites and expansion from Africa

X-chromosomal diversity may reflect climate (when considering human expansion from Africa)

Cranial sexual dimorphism levels in modern humans: Supporting a global expansion originating in southern Africa

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