The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas. We collaborated with six indigenous communities in British Columbia and Southeast Alaska to generate and analyze genome-wide data for over 100 individuals. We then combined this dataset with existing data from populations worldwide, performing an investigation of the genetic structure of indigenous populations of the Pacific Northwest both locally and in relation to continental and worldwide geographic scales. On a regional scale, we identified differences between coastal and interior populations that are likely due to differences both in pre- and post-European contact histories. On a continental scale, we identified differences in genetic structure between populations in the Pacific Northwest and Central and South America, reflecting both differences prior to European contact as well as different post-contact histories of admixture. This study is among the first to analyze genome-wide diversity among indigenous North American populations, and it provides a comparative framework for understanding the effects of European colonization on indigenous communities throughout the Americas.

The Farming/Language Dispersal Hypothesis posits that prehistoric population expansions, precipitated by the innovation or early adop-tion of agriculture, played an important role in the uneven distribution of language families recorded across the world. In this case, the most widely spread language families today came to be distributed at the expense of those that have more restricted distributions. In the Americas, Uto-Aztecan is one such language family that may have been spread across Mesoamerica and the American Southwest by ancient farmers. We evaluated this hypothesis with a large-scale study of mitochondrial DNA (mtDNA) and Y-chromosomal DNA vari-ation in indigenous populations from these regions. Partial correlation coefficients, determined with Mantel tests, show that Y-chromosome variation in indigenous populations from the American Southwest and Mesoamerica correlates significantly with linguistic distances (r= 0.33–0.384;P< 0.02), whereas mtDNA diversity correlates significantly with only geographic distance (r= 0.619;P= 0.002). The lack of correlation between mtDNA and Y-chromosome diversity is consistent with differing population histories of males and females in these regions. Although unlikely, if groups of Uto-Aztecan speakers were responsible for the northward spread of agriculture and their languages from Mesoamerica to the Southwest, this migration was possibly biased to males. However, a recent in situ population expansion within the American Southwest (2,105 years before present; 99.5% confidence interval = 1,273–3,773 YBP), one that probably followed the introduction and intensification of maize agriculture in the region, may have blurred ancient mtDNA patterns, which might otherwise have revealed a closer genetic relationship between females in the Southwest and Mesoamerica.

The systematic relationships of acanthocephalans, including Leptorhynchoides and Pseudoleptorhynchoides that occur in freshwater and marine fishes in Neartic and Neotropical regions, are enigmatic. Leptorhynchoides (3 species) and Pseudoleptorhynchoides (1 species) are presently classified in the Rhadinorhynchidae. However, recent molecular and morphological phylogenies have challenged the monophyly of this family. Sequences of nuclear ribosomal DNA (large subunit, small subunit regions) and the mitochondrial cytochrome c oxidase subunit I gene of Leptorhynchoides thecatus and Pseudoleptorhynchoides lamothei were used in phylogenetic analyses with available sequences of 26 other acanthocephalans. Maximum parsimony and maximum likelihood analyses were identical in placing both genera in the Illiosentidae. Bootstrap analyses also indicate that placement of these genera with members of Illiosentidae is reliably supported.

The allele and haplotype frequencies for 13 Y-chromosome short tandem repeats (STRs) [nine STR loci of the minimal Y-chromosome haplotype (DYS19-DYS385a-DYS385b-DYS3891-DYS38911-DYS390-DYS391-DYS392-DYS393) plus four additional loci (DYS388, DYS426, DYS439, DXYS156)] were determined in 99 males from 4 Panamanian native American populations, including the Chibcha-speaking Ngobe and Kuna and the Choco-speaking Embera and Wounan. Fifty haplotypes were identified, of which 48 (96%) were specific to a single population and 29 (63%) were found in only a single individual. Gene diversity per locus per population ranged from 0 to 0.814, with the highest gene diversity present at the DYS389II locus in the Embera. The haplotypic discrimination capacity was low, ranging from 42.3% in the Kuna to 63.1% in the Wounan. The four tribes showed a high degree of differentiation both at the Y chromosome and in the mitochondrial genome, highlighting the importance of genetic structure even in geographically proximate and linguistically related populations.