Elephant birds and kiwi are sister taxa

Science 23 May 2014, DOI: 10.1126/science.1251981

Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

Alan Cooper group at Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide

The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.

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Y-Chromosome Haplogroup Q: The First Peopling of South America

Battaglia et al. PLoS ONE 8(8): e71390. doi:10.1371/journal.pone.0071390

Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.

American Journal of Human Biology

Article first published online: 4 APR 2013

DOI: 10.1002/ajhb.22382

Microevolution, migration, and the population structure of five Amerindian populations from Nicaragua and Costa Rica

Phillip E. Melton et al.

Objective

This research examines the coevolution of languages and uniparental genetic marker (mitochondrial DNA [mtDNA] and nonrecombining Y-chromosome [NRY]) variation within five Lower Central American (Rama, Chorotega, Maléku, Zapatón-Huetar, and Abrojo-Guaymí) Amerindian groups. This pattern occurred since European contact.

Methods

We examined mtDNA sequence variation from the hypervariable region 1 (HVS-1) and NRY genetic variation using short tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, and DYS439) and NRY haplogroups (Q1a3a, Q1a3*, C3b, R1b1b2, E1b1, G2a2, and I) identified through single-nucleotide polymorphisms. Phylogenetic analysis included multidimensional scaling (MDS), heterozygosity versus r_ii, and analysis of molecular variance (AMOVA).

Results

Eighteen mtDNA haplotypes were characterized in 131 participants with 94.6% of these assigned to the Amerindian mtDNA subclades, A2 and B2. The Amerindian NRY haplogroup, Q1a3a, was present in all five groups and ranged from 85% (Zapatón-Huetar) to 35% (Chorotega). Four populations (Rama, Chorotega, Zapatón-Huetar, and Abrojo-Guaymí) were also characterized by the presence of NRY haplogroup R1b1b2 indicative of western European admixture. Seventy NRY STR haplotypes were identified of which 69 (97%) were population specific. MDS plots demonstrated genetic similarities between Mesoamericans and northern Chibchan Amerindian populations, absent in mtDNA analyses, which is further supported by heterozygosity versus r_ii results.

Conclusions

We conclude that although these linguistically related populations in geographic proximity demonstrate a high degree of paternal genetic differentiation, recent demographic events have dramatically altered the paternal genetic structure of the regions Amerindian populations

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Chuan-Chao Wang

Chuan-Chao Wang

MOE Key Laboratory of Contemporary Anthropology,
School of Life Sciences,
Fudan University,
220# Handan Road, Shanghai 200433, China

Research

1. Molecular Anthropology and Population Structure

The origin and diversification of Chinese and other populations in the Far East is being studied with the genomic tools as well as archaeological, linguistic, historical, and ethnological methods. We have proved the African origin of Chinese, and found two entrances for the early modern human into East Asia, viz, Indo-China peninsula as the major entrance and Altaic Mountain as a minor and late one. Many findings include the contribution rate of the populations from the southern and northern entrances and the migration routes, time and size estimates for the population expansions in East Asian history, gene flows between East and West, finding of the Asian ancestors for Amerinds, genetic relationship between East Asians and the Pacific populations, origin of the Taiwan aborigines, emergence of the Tibetans, etc.

2. Molecular Evolution of Human Genome

Our environmental response system includes, at least, three main components: the immunological response to pathogens or environmental biological factors; the physical anthropological adaptation to physical factors such as sunlight, heat, humidity and so on; and the sensor, metabolism and disposition of environmental chemical factors or xenobiotic substances such as pollutants, carcinogens, pesticide, drug, etc. The environmental exposures such as pathogens and infectious disease have significantly shaped human evolution, and many environmental response genes are reported to have been under positive selection. Evolutionary population genetics and genomic epidemiology of common disease could provide new insight into the function and evolution of disease genes, as well can help decipher the etiology and mechanism of common diseases and understand the differential disease spectrum and drug response between populations and individuals. Coordinated efforts from related fields such as population genetics, molecular evolution, epidemiology, and functional genomics are needed for the study of evolutionary anthropology in era of genomic medicine.

3. Physical Anthropology

The observation and metric items for physical anthropology include all kinds of characters about the appearances of human bodies. Most of those characters are inheritable traits. Genetic methods can be employed to study the genetic modes of these traits, leading to the subsequent genomic locations and the revealing of the secrets of the variations of body shapes and facial features. This is a new field of human biology. We have made some progress with the studies of hair whorls, skin colors, dermatoglyphic patterns, etc. Medical applications of this field will also be studied in the mean time.

4. Ancient DNA study

Abundant population and archaeological resources in China supply a large number of materials for ancient DNA study. DNA information of the ancient human remains provide a view into the genetic landscapes of the past time; animal and plant DNA found from the archaeological sites and on the tools provide information about the lifestyles of ancient people as well as the evolution of the domestic animals and plants. We are collecting ancient DNA information by testing various samples from all over East Asia, setting up the database, and looking into the mist of the history.

5. Ethnology, Archaeology, and Linguistics

Cultures and languages of the human populations developed together with the genetic markers in the history. A combined study of multiple disciplines can better reveal the history and relationships of the ethnic groups, archaeological cultures, and linguistic families, find the correspondence among different systems. From the genetic studies on the population samples from various linguistic families in East Asia, we have found that Y chromosome diversity is strongly associated with linguistic families. Genetic affinities were also found between Daic and Austronesian populations, and also between Hmong-Mien and Mon-Khmer, giving clues to the origin of the relevant linguistic families. On another hand, biostatistic and bioinformatic methods can also be applied to the linguistic data, which can help find the development rules of the languages.

Publications

1. Chuan-Chao Wang, Qi-Liang Ding, Huan Tao, Hui Li^＊(2012) Comment on Phonemic diversity supports a serial founder effect model of language expansion from Africa. Science. 335: 657c.

2. Chuan-Chao Wang, Sara E. Farina, Hui Li^＊ (2012) Neanderthal DNA and Modern Human Origins. Quaternary International. doi:10.1016/j.quaint.2012.02.027.

3. Chuan-Chao Wang, Shi Yan, Zheng Hou, Wenqing Fu, Momiao Xiong, Sheng Han, Li Jin, Hui Li^＊(2012) Present Y chromosomes reveal the ancestry of Emperor Cao Cao of 1,800 years ago. J Hum Genet. 57: 216–218.

4. Chuan-Chao Wang, Shi Yan, Zhen-Dong Qin, Yan Lu, Qi-Liang Ding, Lan-Hai Wei, Shi-Lin Li, Ya-Jun Yang, Li Jin, Hui Li^＊, the Genographic Consortium (2013) Late Neolithic expansion of ancient Chinese revealed by Y chromosome haplogroup O3a1c-002611. J Syst Evol. DOI: 10.1111/j.1759-6831.2012.00244.x.

5. Dongna Li^€, Chuan-Chao Wang^€, Kun Yang, Zhendong Qin, Yan Lu, Xuejing Lin, Hui Li^＊: the Genographic Consortium. (2013). Hainan indigenous substitute for genetic lineages of Champa exile Utsat people. J Syst Evol. DOI: 10.1111/j.1759-6831.2012.12000.x.

6. Shi Yan^＊, Chuan-Chao Wang, Hui Li, Shi-Lin Li, Li Jin^＊, The Genographic Consortium (2011) An updated tree of Y chromosome Haplogroup O and revised phylogenetic position of mutations P164 and PK4. Eur J Hum Genet, 19:1013–1015.

7. Yan Lu, Chuanchao Wang, Zhendong Qin, Bo Wen, Sara E. Farina, Li Jin, Hui Li^＊, the Genographic Consortium. (2012) Mitochondrial Origin of the Matrilocal Mosuo People in

China. Mitochondrial DNA. 23(1):13-19.

8. Longli Kang, Yan Lu, Chuanchao Wang, Kang Hu, Feng Chen, Kai Liu, Shilin Li, Li Jin^＊, Hui Li^＊ and the Genographic Consortium (2012) Y chromosome O3 Haplogroup Diversity in Sino-Tibetan Populations Reveals Two Migration Routes into the Eastern Himalayas. Ann Hum Genet, 76(1):92-99.

9. Yan Lu ^€, Longli Kang ^€, Kang Hu, Chuanchao Wang, Xiaoji Sun, Feng Chen, Judith R Kidd, Kenneth K Kidd, Hui Li^＊ (2012) High diversity and no significant selection signal of human ADH1B gene in Tibet. Investigative Genetics 3:23.

10. Yan Lu ^€, Shang-Ling Pan ^€, Shu-Ming Qin, Zheng-Dong Qin, Chuan-Chao Wang, Rui-Jing Gan, Hui Li^＊, the Genographic Consortium. (2013). Genetic evidence for the multiple origins of Pinghua Chinese. J Syst Evol. DOI: 10.1111/jse.12003.

11. Xiaoyun Cai ^€, Zhendong Qin ^€, Bo Wen, Shuhua Xu, Yi Wang, Yan Lu, Lanhai Wei,

Chuanchao Wang, Shilin Li, Xingqiu Huang, Li Jin, Hui Li^＊: the Genographic consortium (2011) Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes. PLoS ONE, 6(8): e24282.

12. Qi-Liang Ding, Chuan-Chao Wang, Sara E. Farina, Hui Li^＊(2011) Mapping Human Genetic

Diversity on the Japanese Archipelago. Advances in Anthropology, 1(2)19-25.

13. 王传超，严实，韩昇，金力，李辉^＊（2012）鄱阳操姓血缘上并非出自曹操. 现代人类学通讯.6:e2/14-17.

14. 王传超，严实，侯铮，傅雯卿，熊墨淼，韩昇，金力，李辉^＊ (2011) Y 染色体揭开曹操

身世之谜. 现代人类学通讯. 5:e17/107-111.

15. 王传超, 李士林, 周怀谷, 平原, 李辉^＊ (2011) 将DNA 鉴定技术正确应用于司法实践—

—反驳《DNA 难堪“证据之王”之责》一文. 中国社会科学报. 164:7.

16. Chuanchao Wang, Hui Li^＊ (2010) Are Neanderthals challenging the “out-of-Africa” model for modern human origins? First Human Settlements in Eurasia. EXPO Spanish Pavilion, Shanghai,

October 8‐10, 2010. Session 2.1: Taxonomy and phylogeny.

17. Pritchard Jonathan K. Chuanchao Wang, Hui Li^＊ (Chinese translation) (2010) How we are

evolving? Globalscience, Chinese Edition of Scientific American. 59(11):19‐25.

18. 王传超, 李辉^＊ (2010) 古DNA 分析技术发展的三次革命. 现代人类学通讯. 4:e6/35-42.

19. 王传超, 严实, 李辉^＊ (2010) 姓氏与Y 染色体. 现代人类学通讯. 4:e5:27-34.

20. 王传超, 严实, 李辉^＊ (2010) Y 染色体与姓氏宗族演变. 科学时报 2010 年5 月12 日A2版.