Rene J. Herrera's research while affiliated with Colorado College and other places

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Publications (329)


Geographical and frequency distribution of haplogroup O2a2b-P164. The list of populations and their codes are in Supplementary Table 1. Percentages in parenthesis are the haplogroup O2a2b-P164 frequencies in each polulation.
Distribution of O2a2b-P164 haplogroup frequencies and diersity values. The X and Y axes represent longitude and latitude respectively. The scales on the rightr side of the plots represent haplogroup frequency (A), Vp diversity (B) and Nei's diversity (C) values. The list of populations and their codes are in Supplementary Table 1.
MDS plot of O2a2b-P164 haplogroup populations based on Y-STR Rst genetic distance. The list of populations and their codes are in Supplementary Table 1.
O2a2b-P164 haplogroup Y-STR haplotype network based on 15 Y-STR s. The list of populations, their codes and their groupings are in Supplementary Tables 1 and 2. Circles represent a haplotype. The size of the circle is proportional to the sample size. The length of the lines is proportional to the number of differences between haplotydes. Nodes without circles represent medial vectors which are hypothetical haplotydes/nodes which connect one haplotyde to the next. Black circles mark the roots of subgroups I, II and III.
O2a2b-P164 haplogroup Y-STR haplotype network for Polynesia and Micronesia based on 15 Y-STRs. The list of populations, their codes and their groupings are in Supplementary Table 1.

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Delineating the dispersal of Y-chromosome sub-haplogroup O2a2b-P164 among Austronesian-speaking populations
  • Article
  • Full-text available

January 2024

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180 Reads

Scientific Reports

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Göran Runfeldt

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Rene J. Herrera

This article reports on an exploration of the Y-chromosome sub-haplogroup O2a2b-P164 in Austronesian-speaking populations. Moderate to high abundance of the P 164 mutation is seen in the West Pacific including the Amis of Formosa (36%) and the Filipinos of Mindanao (50%) as well as in the Kiritimati of Micronesia (70%), and Tonga and Samoa of West Polynesia (54% and 33%, respectively), and it drops to low frequencies in populations of East Polynesia. The communities of Polynesia and Micronesia exhibit considerable inter- and intra-population haplotype sharing suggesting extensive population affinity. The observed affinities, as well as the ages and diversity values within the P 164 sub-haplogroup among Austronesian-speaking populations signal an ancestral migration route and relationships that link the Amis of Taiwan with distant communities in West and East Polynesia, Micronesia, and the Maori of New Zealand. High resolution sequencing of the Austronesian Y chromosome indicate that the P 164 lineage originated about 19,000 ya and then split into three branches separating the Ami aborigines, Southeast Asian and Polynesian/Micronesian populations about 4700 ya, roughly coinciding with the initiation of the Austronesian diaspora. The Y-chromosomes of all the Polynesian and Micronesian population examined belong to the new FT 257096 haplogroup.

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Bidirectional dispersals during the peopling of the North American Arctic

January 2023

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181 Reads

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2 Citations

Scientific Reports

It is thought that Paleo-Inuit were the first people that settled the American Arctic about 5000 BP (before the present) from a migration that crossed Beringia from Northeast Asia. It is theorized that this group initially migrated to the North Slopes of Alaska and subsequently expanded eastward, eventually reaching Greenland. A second circumpolar dispersal of Neo-Inuit from the North Slopes associated with the Thule-Inuk culture has been postulated to have extended eastward around 800 BP, totally replacing the original Paleo-Inuit without admixing. Although generally accepted, this migration scenario is incompatible with previously reported indications of east to west gene flow across the American Arctic. Here we report on the Y-chromosome haplogroup and Y-STR diversity of the four circumpolar populations of the Tuva Republic (N = 24), Northeast Siberia (N = 9), Bethel, Alaska (N = 40), and Barrow, Alaska (N = 31). Four haplogroup lineages (Q-NWT01, Q-M3, Q-M346, and Q-M120) were detected, Q-NWT01 and Q-M3 being the most abundant at 11.11 and 66.67% in Northeast Siberia, 32.50 and 65.00% in Bethel, and 67.74 and 32.26% in Barrow, respectively. The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STYR loci using the AmpFlSTR Yfiler system. Age estimates and diversity values for the Q-NWT01 and Q-M3 mutations suggest extensive movement of male individuals along the entire longitudinal stretch of the American circumpolar region. Throughout the entire region, Q-M3 exhibits a west to east decreasing gradient in age and diversity while Q-NWT01 indicates the opposite with older TMRCA and higher diversity values running from east to west with the most recent estimates in Canada and Alaska. The high age and diversity values in Greenland are congruent with an origin of the Q-NWT01 mutation in the east of the circumpolar range about 2000–3000 ya. This scenario is incompatible with a complete biological replacement starting about 700 BP of Paleo-Inuit like the Dorset by the Thule-Inuit (Neo-Inuit), as is currently thought, and more parsimonious with gene flow carrying the NWT01 mutation from a pre-Thule population to the ancestors of the present-day Inuit.


On the Y chromosome of Chennai, Tamil Nadu and the Indian Subcontinent

January 2023

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226 Reads

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1 Citation

Gene

Several migratory waves from various origins along with cultural practices restricting marriages between peoples of different castes and tribes as well as continued endogamy have led to a complex and diverse society in the Indian subcontinent. Despite being widely represented in genetic studies, several interrogatives remain with regards to India's current genetic constituents and distributions, source populations and population relationships. To identify the forces that may have shaped Indian population's genetic relationships, we undertook a comprehensive comparative study of the Y-chromosomes across India utilizing Y-STR and Y-SNP chromosomal markers using the general population of Chennai in the state of Tamil Nadu as a point of reference. Our analyses identify differences in source populations for different regions within India, unique linguistic characteristics as well as demographic and cultural forces that may have shaped population structure.









Citations (12)


... Haplogroup a representative of the Paleo-Eskimo Sakkak culture who lived in Greenland about 4 thousand years ago (Rasmussen et al., 2010). Currently, haplogroup Q-B143 is distributed only among the indigenous populations of the American Far North, Greenland and Siberia (Malyarchuk et al., 2011;Karmin et al., 2015;Grugni et al., 2019;Luis et al., 2023). In the Koryaks of the Magadan region, this Q haplogroup was detected with a frequency of 16.7 % (see Table 1). ...

Reference:

Genetic history of the Koryaks and Evens of the Magadan region based on Y chromosome polymorphism data
Bidirectional dispersals during the peopling of the North American Arctic

Scientific Reports

... Given the importance of the use of Y-STR in forensic analysis, extensive population databases of haplotype frequencies are necessary to allow for calculating the probability of coincidence between two genetic profiles, and an analysis of the possible population substructure, both highly dependent on the amount of information available. In addition to the existence of a large number of publications with the participation of numerous laboratories around the world (for example, Chen et al. 2018;Caputo et al. 2019;Jankova et al. 2019;Ambrosio et al. 2020;Claerhout et al. 2020;Hakim et al. 2020;Adnan et al. 2020;Bini et al. 2021;Fang et al. 2021;Babić Jordamović et al. 2021;Neyra-Rivera et al. 2021;Adnan et al. 2022;Albarzinji et al. 2022;Ashirbekov et al. 2022;Dooley et al. 2022;Mihajlovic et al. 2022;Pamjav et al. 2022;Tätte et al. 2022;Ashirbekov et al. 2023;Lee et al. 2023), an online database was created, the YHRD-Y chromosome haplotype reference database (https://yhrd.org/) containing haplotype profiles of the markers most used in forensic genetics, for a high number of populations. ...

Genetic characterization of populations in the Marquesas Archipelago in the context of the Austronesian expansion

Scientific Reports

... DNA extraction from swabs of 6 samples 6 from Taiwan (n = 2, TW 102 and TW 106), Kiritimati (n = 3, TARA 89, TARA 97 and TARA 134) and the Marquesas (n = 1, NH 10 ) was performed using the standard phenol-chloroform method and ethanol-precipitated as described previously 13 . A NanoDrop 1000 Spectrophotometer (Thermo Scientific) was used for DNA quantitation. ...

Post-Austronesian migrational wave of West Polynesians to Micronesia
  • Citing Article
  • February 2022

Gene

... Therefore, the X-STR results provided here have proved to be complementary to other studies, eg based on the Y-chromosome, on these populations. Furthermore, our findings are in accordance with the autosomal analysis of the populations of Sousse and Makthar published by Al- Haj-Taib et al. (2021), that has proven the differentiation of North-African cluster from different European populations. ...

Genetic analysis of sixteen autosomal STR loci in three Tunisian populations from Makthar, Nabeul and Sousse
Annals of Human Biology

Annals of Human Biology

... These regions are characterized by distinct genetic, cultural, and environmental factors that may contribute to the increased incidence of β thalassemia. The population of western Indonesia has higher percentages of an Austronesian/Malay genetic makeup, while eastern Indonesians have higher percentages of Melanesian genetics [47]. Western Indonesians are more heavily influenced by trade/cultures from mainland Asia, while the eastern culture reflects more isolated island developments. ...

The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations
  • Citing Article
  • March 2021

European Journal of Human Genetics

... The reason for the two analyses was because of the increased number of markers in the analyzed population and the reduced number of markers in the populations that were available for comparison. The first group of populations selected for comparison with the population of Croatia using the Yfiler™ Plus marker set included: Croatia (n = 507, present study), Slovenia (n = 194, (22)), Belgium (n = 160, (23)(24)(25)(26)), Hungary (n = 218, (27)(28)(29)(30)(31)(32)(33)), Austria (n =392, (34)(35)(36)(37)(38)), Germany (n = 495, (39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)), Italy (n = 689, (50)(51)(52)(53)(54)(55)(56)(57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67)), North Macedonia (n = 295, (68)(69)(70)(71)), Serbia (n = 183, (72-74)), Denmark (n=177, (75)), Ethiopia (n=290, (76)), French Polynesia (n=81), (77,78)), Ghana (n=584, (79)), India (n=541, (80)(81)(82)(83)(84)(85)(86)(87)(88)(89)(90)(91)(92)(93)(94)(95)(96)(97)(98)), Lithuania (n=251, (99)(100)(101)), Mexico (n=354, (102)(103)(104)(105)(106)(107)), Nigeria (n=337, (108)), Pakistan (n=280, (109)(110)(111)(112)(113)(114)(115)(116)(117)(118)(119)(120)(121)), Poland (n=612, (122)(123)(124)(125)(126)(127)(128)(129)(130)), Russian Federation (n=958, (131)(132)(133)(134)(135)(136)(137)(138)(139)(140)(141)(142)(143)), Saudi Arabia (n=156, (144,145)), Spain (n=316, (146)(147)(148)(149)(150)(151)(152)(153)(154)(155)(156)(157)(158)(159)(160)(161)(162)(163)(164)), Switzerland (n=724, (19,165,166)), and United Kingdom (n=115, (167,168)). ...

The Y chromosome of autochthonous Basque populations and the Bronze Age replacement

Scientific Reports

... The most recent census estimates the Soliga population to be around 36,000. The Soliga tribal might be one of the earliest inhabitants of this region and, along with several other tribal communities in southern Indiagenetic to Australian aboriginal populations [22]. We included human settlements located within BR Hills and MM Hills Forest areas, as well as settlements within a 5 km radius of the forest boundary. ...

The Y-chromosome of the Soliga, an ancient forest-dwelling tribe of South India

Gene

... Considering the wide presence of sub-haplogroup O2a2-P164 among MSEA, ISEA and Indonesian populations 37 , we undertook an exploration of its distribution in Micronesia 13 , West 26 , East 38 and Southwest Polynesia 39 (see Fig. 1 for location and frequency distribution). Contour maps were constructed to illustrates the distribution of frequencies and diversities in Near and Far Oceania (Fig. 2, panels A, B and C). ...

The Marquesans at the fringes of the Austronesian expansion
  • Citing Article
  • January 2019

European Journal of Human Genetics

... Buccal swabs were processed utilizing the Gentra Buccal Cell Kit (Puregene, Gentra Systems, Minneapolis, MN) according to the manufacturers' specifications. NanoDrop 1000 Spectrophotometer (Thermo Scientific) was used for DNA quantitation 21 . All samples were procured from donors voluntarily with informed consent while closely adhering to the ethical guidelines stipulated by Colorado College, Colorado Springs, Colorado USA and following the ethical principles and guidelines of the Declaration of Helsinki for the protection of human subjects. ...

Cebú, Thailand and Taiwanese aboriginal populations according to Y-STR loci

Gene

... The QTP is the youngest and largest plateau in the world covering most of Qinghai Province and Tibet of China, with a mean elevation of 4500 m (Zheng 1996), surrounded by several vast mountain ranges (Himalayan, Kunlun, Qilian, Karakoram and Hengduan Mountains) (Rowold et al. 2019). A common hypothesis for the rich of mountain biodiversity is uplift-driven diversity, which means that geological events created the conditions for speciation (Hoorn et al. 2013;Schwery et al. 2014;Favre et al. 2015;Hughes 2016;Lagomarsino et al. 2016). ...

Investigating the genetic diversity and affinities of historical populations of Tibet
  • Citing Article
  • September 2018

Gene