George H. Perry

The population of Madagascar exhibits a globally unique combination of African and Asian genetic ancestries. Previous studies have described the admixture history of Madagascar at island-wide scales [1,2], but less focus has been paid to fine-scale population structure across the island. We present new genome-wide genetic data from 192 individuals sampled across five regions of Madagascar. We identify population structure at extremely fine spatial scales (~10 km) among the Merina of the central highlands. By analysing subpopulations separately, we found one Merina group exhibited similarity to coastal populations in f4 ratios, estimated admixture dates, and pairwise FST distances, while another group was similar to other highland individuals in the same measures. This fine-scale substructure is likely associated with historical coastal-to-highland migration during the 18th and 19th centuries. In contrast, we also observe macro-scale structure in estimated timing of admixture across the island, with southeastern coastal groups exhibiting the earliest estimated admixture timings, and northern groups exhibiting the latest. This pattern corroborates previous results [1,2], and may suggest differing histories of admixture timing among Malagasy populations. Our results emphasise the importance of deep micro-geographic sampling to complement macro-scale analysis when characterising demographic history.

Understanding the process of genetic adaptation in response to human-mediated ecological change will help elucidate the eco-evolutionary impacts of human activity. In the 1930s red imported fire ants (Solenopsis invicta) were accidently introduced to the Southeastern USA, where today they are both venomous predators and toxic prey to native eastern fence lizards (Sceloporus undulatus). Here, we investigate potential lizard adaptation to invasive fire ants by generating whole-genome sequences from 420 lizards across three populations: one with long exposure to fire ants, and two unexposed populations. Signatures of positive selection exclusive to the exposed population overlap immune system, growth factor pathway, and morphological development genes. Among invaded lizards, longer limbs (used to remove stinging ants) are associated with increased survival. We identify alleles associated with longer limbs that are highly differentiated from the unexposed populations, a pattern counter to the pre-invasion latitudinal cline for limb lengths based on museum specimens. While we cannot rule out other environmental differences between populations driving these patterns, these results do constitute plausible genetic adaptations in lizards invaded by fire ants.

Coral reefs are declining worldwide due to anthropogenic-driven environmental change. The foundation and health of these ecosystems rely on the harmonious functioning of all members of coral holobionts, i.e., cnidarian host, symbiotic microalgae, and associated microbiome. Coral stress responses often involve shifts in the taxonomic identity of their symbionts and microbiomes. Tracing back changes in coral holobiont composition over prolonged time periods can help us reconstruct health history of reefs and gain a better understanding of coral response to current stressors. Here, we focused on a major Caribbean reef-builder coral, Orbicella faveolata , from the Varadero Reef, Colombia. This reef has undergone extensive freshwater sediment discharge for decades as result of urbanization. We show, for the first time, that paleogenomic and paleoclimatic approaches can be combined to reconstruct historical, coral holobiont dynamics potentially associated with anthropogenic disturbances.

Latiné people differ markedly in our lived experiences in ways that are underappreciated. Meanwhile, variations in social experiences are known to be associated with differential health outcomes. We test whether immigration history is associated with health differences among U.S.-based Cuban refugees. Cubans from the circum-1980 Mariel Boatlift migration wave reported significantly higher instances of disability than Early Cuban Exiles, Freedom Flight refugees, and Special Period refugees. We also interviewed Miami-based Cubans. Participants described heightened discrimination in 1980s Cuba and U.S., which we hypothesize contributed to higher instances of disability refugees of that era. By understanding how differential social experiences shape health, we aim to provide a nuanced understanding of the social determinants of health and the ways adverse experiences can be combated. One-Sentence Summary Even within a Latiné community from a single country of origin, we find that differential social experiences of immigrating to the U.S. are associated with variation in health outcomes.

Understanding the process of genetic adaptation in response to human-mediated ecological change will help elucidate the eco-evolutionary impacts of human activity. Red fire ants ( Solenopsis invicta ) spread across Southeastern USA since their accidental introduction via Port Mobile, Alabama in the 1930s, serving today as both novel venomous predator and novel toxic prey to native eastern fence lizards ( Sceloporus undulatus ). To identify potential signatures of genetic adaptation in lizards to invasive fire ants, we generated whole genome sequencing data from 420 native fence lizards sampled across three populations, two of which had not been invaded by fire ants (in Tennessee and Arkansas) and one which had been invaded for ∼70 years (Alabama). We detected signatures of positive selection exclusive to the exposed Alabama population for genetic variants overlapping genes related to the membrane attack complex of the complement immune system, growth factor pathways, and morphological development. Prior work identified a relationship between increased lizard survival of fire ant attack and longer hind limbs, which lizards use to remove ants from their bodies. Furthermore, we conducted a genome-wide association study with 381 Alabama lizards to identify 24 hind limb length-associated genetic loci. For two loci, positive-effect alleles occur in high frequency and overlap genomic regions that are highly differentiated from the populations naïve to fire ants. Collectively, these findings represent plausible genetic adaptations in response to fire ant invasion, whereby morphological differentiation may increase survival against swarming ants and altered immune responses may allow the exploitation of a novel, toxic food resource. Significance statement: Human activity can force interactions between species from distinct ecological backgrounds. These interactions can consequently impose novel selective pressures on endemic populations via predation or disruption of ecological niches through community-wide effects. While some endemic taxa have been able to adapt biologically to these disruptions, we do not have a full understanding of the underlying genetic processes that may allow it. Here we identify genomic signatures of recent adaptation nearby genes involved in morphological and immunological processes in native fence lizards that are consistent with pressures imposed by the venomous, predatory fire ants introduced by humans. These signatures are largely absent from lizard populations that are naïve to fire ants.

Significance: Subsistence shifts from hunting and gathering to agriculture over the last 12,000 y have impacted human culture, biology, and health. Although past human health cannot be assessed directly, adult stature variation and skeletal indicators of nonspecific stress can serve as proxies for health during growth and development. By integrating paleogenomic genotype and osteological stature data on a per-individual basis for 167 prehistoric Europeans, we observe relatively shorter than expected statures among early farmers after correcting for individual genetic contributions to stature. Poorer nutrition and/or increased disease burdens for early agriculturalists may partly underscore this result. Our integrated osteological–genetic model has exciting potential for studies of past human health and expansion into various other contexts.

Objectives: The Holocene arrival of humans on Madagascar precipitated major changes to the island's biodiversity. The now‐extinct, endemic “subfossil” megafauna of Madagascar were likely hunted by early human inhabitants. Perhaps in part due to preferential hunting of larger prey, no surviving endemic species on Madagascar is >10 kg. Moreover, some subfossil bones of extant lemurs are considerably larger than those of the modern members of their species, but subfossil versus modern locale differences for the comparisons conducted to date lead to uncertainty about whether these size differences reflect in situ change or pre‐existing ecogeographic variation. Here, we revisited this question with samples from nearby locales.Materials and Methods: We used high‐resolution 3D scan data to conduct comparative morphological analyses of subfossil and modern skeletal remains of one of the larger extant lemurs, Verreaux's sifakas (Propithecus verreauxi) from subfossil and modern sites only ~10 km apart: Taolambiby (bones dated to 725–560—1075–955 cal. years before present) and Beza Mahafaly Special Reserve, respectively.Results: The mean aggregate score for all subfossil elements (n = 12; 0.089 ± 0.117) is significantly greater than that for the modern individuals (n = 31; 0.009 ± 0.045; t‐test; p = 0.039). We found that the average subfossil sifaka bone is ~9% larger than that of modern sifakas (permutation test p = 0.037).Discussion: We cannot yet conclude whether this size difference reflects evolutionary change or an archaeological aggregation/taphonomic process. However, if this is a case of phyletic dwarfism in response to human size‐selective harvesting pressures then the estimated rate of change is greater than those previously calculated for other archaeological cases of this phenomenon.

High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

In recognition that evolutionary theory is critical for understanding modern human health, eLife is publishing a special issue on evolutionary medicine to showcase recent research in this growing and increasingly interdisciplinary field.

Significance: Based on “subfossil” skeletal remains it is known that multiple now-extinct giant lemur (primate) species with estimated body masses of up to ∼160 kg survived on Madagascar into the past millennium. In this study, we used ancient DNA methods to sequence the nuclear genome of one of these megafaunal lemurs,Megaladapis edwardsi(∼85 kg). With the power of the nuclear genome, we robustly resolved the phylogenetic relationship betweenMegaladapisand other lemurs, which had been a lingering uncertainty. We also identified multiple signatures of past positive natural selection across theM. edwardsigenome that support reconstructions of this taxon as a large-bodied, specialized folivore.