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1. Tracing demographic histories through time using ancient DNA in Chilean Fuego-Patagonia

   Balentine, C. M. ; Alfonso-Durruty, M. ; Reynolds, A. W. ; Vilar, M. ; Morello, F. ; San Román, M. ; Springs, L. C. ; Bolnick, D. A. ( January 2022 , American Journal of Biological Anthropology)

   Historically, hunter-gatherers living east and west of the Andean foothills of southern South America (Fuego-Patagonia) practiced different subsistence strategies. To the east, the wide open and relatively dry pampas presented a climate ideal for Terrestrial hunter-gatherers who depended on terrestrial animals (e.g., Lama guanicoe). In contrast, Marine hunter-gatherers who lived on islands in the western archipelago, a colder and wetter environment, mainly subsisted on marine resources (e.g., seals and shellfish). Archaeological evidence dates Terrestrial hunter-gatherers’ presence in Fuego-Patagonia to at least ~10,500 BP, whereas Marine hunter-gatherers’ presence dates to ~6,500 BP and is associated with highly specialized tools that have only been observed in the archaeological record after this time. Genetic analyses of some ancient Fuegian-Patagonians have supported the hypothesis that Marine hunter-gatherers migrated into the region after Terrestrial hunter-gatherers, around 6,500 BP (7,500 calBP), while analyses of other individuals suggest that Marine hunter-gatherers descended from the earlier Terrestrial hunter-gatherer groups. Here, we test these hypotheses by analyzing newly collected genome-wide data from n=46 ancient Chilean Fuegian-Patagonian individuals belonging to Marine, Terrestrial, and Mixed-economy archaeological sites dating to 6,895–304 calBP. We explored basic population structure among these hunter-gatherer groups using PCA and ADMIXTURE. We calculated π, pairwise-FST, and f-statistics, and developed demographic simulations to further examine genetic relationships among the groups. The results of this study shed light on local demographic patterns of ancient southern South American groups, which in turn provides more insight into broader population histories of South America. This study was funded by FONDECYT (Chile), National Geographic Society, National Science Foundation, and Wenner-Gren Foundation. C. M. Balentine is supported by an NSF Graduate Research Fellowship. 

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2. Old divergence and restricted gene flow between torrent duck ( Merganetta armata ) subspecies in the Central and Southern Andes

   https://doi.org/10.1002/ece3.5538  

   Alza, Luis ; Lavretsky, Philip ; Peters, Jeffrey L. ; Cerón, Gerardo ; Smith, Matthew ; Kopuchian, Cecilia ; Astie, Andrea ; McCracken, Kevin G. ( August 2019 , Ecology and Evolution)

   To investigate the structure and rate of gene flow among populations of habitat‐specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction.

   Peruvian and Argentine Andes.

   Two subspecies of torrent duck (Merganetta armata).

   We sampled 156 individuals in Peru (M. a. leucogenis;Chillón River,n = 57 and Pachachaca River,n = 49) and Argentina (M. a. armata;Arroyo Grande River,n = 33 and Malargüe River,n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine‐scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru,n = 10 and Argentina,n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z‐linked double‐digest restriction‐associated DNA sequences.

   Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species‐level differences (Φ_STmtDNA = 0.82; Φ_STautosomal = 0.30; Φ_STZ chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using∂a∂i(isolation‐with‐migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal∂a∂i = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well‐differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country.

   We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure.

    

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3. Sex‐biased parental investment and female wealth accumulation in ancient California

   https://doi.org/10.1002/ajpa.24806  

   Greenwald, Alexandra M. ; Burns, Gregory R. ; Eerkens, Jelmer W. ; Bartelink, Eric J. ; Leventhal, Alan ; Arellano, Monica V. ( July 2023 , American Journal of Biological Anthropology)

   The mortuary record at Middle Period siteKalawwasa Rummeytak(CA‐SCL‐134) (2600‐1225 cal BP) in California's southern Santa Clara Valley shows pronounced wealth inequality;Olivellashell bead wealth, as well as other grave goods, are concentrated in the burials of several older adult females. The concentration of wealth among women, along with regional strontium isotopic evidence of male‐biased residential shifts in early adulthood, suggests a matrilineal kinship system that practiced matrilocal post‐marital residence patterns. We suggest local resource enhancement effects incentivized keeping women in their natal communities and investing more in female offspring.

   With the consent of, and in collaboration with, the Muwekma Ohlone Tribe of the San Francisco Bay Area, this paper employs isotopic analysis (δ¹⁵N andδ¹³C,⁸⁶Sr/⁸⁷Sr) to examine duration of exclusive breastfeeding, weaning age (complete cessation of breastmilk consumption), early childhood diet, and lifetime residential mobility of individuals interred atKalawwasa Rummeytakto test the assumption that the site inhabitants favored matrilocality and that female offspring received greater levels of investment in groups with female wealth/status attainment. First molars, third molars, and bone was sampled from 22 individuals.

   The average weaning age for females atKalawwasa Rummeytakis 36.3 months ± 9.7 (1 SD), or just over 3 years. The average weaning age for males is 31.2 ± 7.9 months (1 SD), or about 2.6 years. Infants at the site were provisioned with supplemental foods dominated by C₃plants and terrestrial herbivores, as well as anadromous fish. After weaning, individuals consumed a diet dominated by acorns, C₃plants, and terrestrial herbivores, with periodic inclusion of anadromous fish. 30% of the sampled population of females exhibit local first molar⁸⁷Sr/⁸⁶Sr values, suggesting thatKalawwasa Rummeytakis their natal community. None of the males interred at the site are locals.

   Despite the small sample size often unavoidable in archaeological contexts, we find possible female‐biased parental investment strategies. Cessation of breastfeeding (weaning) was, on average, 5 months earlier for males compared to females. There are no differences between females and males in the consumption of supplemental or post‐weaning foods. Strontium data suggest a flexible postmarital residence system that favored matrilocality. This may have incentivized greater investment in female offspring.

    

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4. Ancient and modern genomics of the Ohlone Indigenous population of California

   https://doi.org/10.1073/pnas.2111533119  

   Severson, Alissa L. ; Byrd, Brian F. ; Mallott, Elizabeth K. ; Owings, Amanda C. ; DeGiorgio, Michael ; de Flamingh, Alida ; Nijmeh, Charlene ; Arellano, Monica V. ; Leventhal, Alan ; Rosenberg, Noah A. ; et al ( March 2022 , Proceedings of the National Academy of Sciences)

   Traditional knowledge, along with archaeological and linguistic evidence, documents that California supports cultural and linguistically diverse Indigenous populations. Studies that have included ancient genomes in this region, however, have focused primarily on broad-scale migration history of the North American continent, with relatively little attention to local population dynamics. Here, in a partnership involving researchers and the Muwekma Ohlone tribe, we analyze genomic data from ancient and present-day individuals from the San Francisco Bay Area in California: 12 ancient individuals dated to 1905 to 1826 and 601 to 184 calibrated years before the present (cal BP) from two archaeological sites and eight present-day members of the Muwekma Ohlone tribe, whose ancestral lands include these two sites. We find that when compared to other ancient and modern individuals throughout the Americas, the 12 ancient individuals from the San Francisco Bay Area cluster with ancient individuals from Southern California. At a finer scale of analysis, we find that the 12 ancient individuals from the San Francisco Bay Area have distinct ancestry from the other groups and that this ancestry has a component of continuity over time with the eight present-day Muwekma Ohlone individuals. These results add to our understanding of Indigenous population history in the San Francisco Bay Area, in California, and in western North America more broadly. 

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5. Leap‐frog dispersal and mitochondrial introgression: Phylogenomics and biogeography of Limnonectes fanged frogs in the Lesser Sundas Archipelago of Wallacea

   https://doi.org/10.1111/jbi.13526  

   Reilly, Sean B. ; Stubbs, Alexander L. ; Karin, Benjamin R. ; Bi, Ke ; Arida, Evy ; Iskandar, Djoko T. ; McGuire, Jimmy A. ( February 2019 , Journal of Biogeography)

   The Lesser Sunda Islands are situated between the Sunda and Sahul Shelves, with a linear arrangement that has functioned as a two‐way filter for taxa dispersing between the Asian and Australo‐Papuan biogeographical realms. Distributional patterns of many terrestrial vertebrates suggest a stepping‐stone model of island colonization. Here we investigate the timing and sequence of island colonization in Asian‐origin fanged frogs from the volcanic Sunda Arc islands with the goal of testing the stepping‐stone model of island colonization.

   The Indonesian islands of Java, Lombok, Sumbawa, Flores and Lembata.

   Limnonectes dammermaniandL. kadarsani(Family: Dicroglossidae)

   MitochondrialDNAwas sequenced from 153 frogs to identify major lineages and to select samples for an exon‐capture experiment. We designed probes to capture sequence data from 974 exonic loci (1,235,981 bp) from 48 frogs including the outgroup species,L. microdiscus. The resulting data were analysed using phylogenetic, population genetic and biogeographical model testing methods.

   The mtDNAphylogeny findsL. kadarsaniparaphyletic with respect toL. dammermani, with a pectinate topology consistent with the stepping‐stone model. Phylogenomic analyses of 974 exons recovered the two species as monophyletic sister taxa that diverged ~7.6 Ma with no detectable contemporary gene flow, suggesting introgression of theL. dammermanimitochondrion intoL. kadarsanion Lombok resulting from an isolated ancient hybridization event ~4 Ma. WithinL. kadarsani,the Lombok lineage diverged first while the Sumbawa and Lembata lineages are nested within a Flores assemblage composed of two parapatrically distributed lineages meeting in central Flores. Biogeographical model comparison found strict stepping‐stone dispersal to be less likely than models involving leap‐frog dispersal events.

   These results suggest that the currently accepted stepping‐stone model of island colonization might not best explain the current patterns of diversity in the archipelago. The high degree of genetic structure, large divergence times, and absent or low levels of migration between lineages suggests thatL. kadarsanirepresents five distinct species.

    

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