Comparative genomics uncovers the evolutionary history,demography, and molecular adaptations of South American canids

The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.

The arrival and diversification of mammals in South America during the 66-My history of the Cenozoic has long interested paleontologists and evolutionary biologists (1). The immigration of carnivorous mammals such as canids, felids, procyonids, and ursids from North America into South America during the Great American Biotic Interchange in the Pliocene was especially noteworthy and led to the turnover and extinction of many endemic species, facilitating the diversification of the colonizing lineages. As a primary example, South America harbors the most diverse extant canid community, with 10 currently recognized species (2), including disparate forms such as the squat bush dog and the long-legged maned wolf (Fig. 1). Due to their rapid and relatively recent diversification, three fundamental aspects of their evolutionary history remain uncertain.Open in a separate windowFig. 1.Species tree and ancestral area reconstruction of SA canids. The species tree was estimated by applying ASTRAL-III (45) to 6,716 genomic windows (25 kb each). A total of 31 genomes were included in the analysis (SI Appendix, Table S1), but only the clade containing SA canids is shown here (see complete tree in SI Appendix, Fig. S1). All nodes had 100% bootstrap support based on 100 replicates. The best-fitting BioGeoBEARS (46) model was DIVALIKE (dispersal vicariance) with the parameter “J” that represents a founder event (SI Appendix, Fig. S2 and Table S2). Colored boxes on each node indicate estimated ancestral ranges, while boxes at terminal branches indicate current species distribution (“e,” east of the Andes; “c,” central region of the Andes; and “w,” west of the Andes). The probabilities of these ancestral regions are shown in the pie charts below each node. Purple-colored pie charts indicate a distribution on the west and east of the Andes. The maps on the Right represent the distribution of species within three major clades. The colored distributions on the map match the colors underlining species names. Canid illustrations from ref. 2 are used with permission from Princeton University Press.First, the pattern of invasion and dispersion of canids into South America is poorly defined. Although it is widely agreed that the first canids migrated into South America using the Panama land bridge, when this migration event occurred is uncertain. Molecular, fossil, and geological data suggest that several terrestrial dispersal events may have occurred prior to the generally cited estimate of approximately 3 Mya for the complete formation of the land bridge (3–5). There is also uncertainty about the number of ancestral lineages that entered South America and the antiquity of their diverse adaptations (6–13). The Andes were close to their present-day elevation 6 Mya in the Late Miocene (14). Therefore, when canids arrived in South America, the Andes formed a distinct geographic barrier that extended along the length of the continent (9, 13, 15–19). Although canids are found on both sides of the Andes, the ancestral canid lineage could have entered the east or west side of the Andes or both sides simultaneously and subsequently diversified. Knowing the number of invasions and dispersion of canid lineages in South America is critical to understanding the timing, interrelationships, and environmental correlates underlying this burst of speciation.Second, the extent and timing of speciation and lineage-specific demographic history, including the potential impact of substantial climatic differences on each side of the Andes, are not well understood. Along the eastern lowlands, the glacial periods of the Pleistocene led to an expansion of savanna vegetation into areas that now support forest (20–23). To the west, glacial periods caused the expansion of glaciers in the south and shifts of vegetation zones along the Andean slopes (24–26). These changes likely reduced the availability of favorable habitats for some canid species but extended the distribution of others (20, 27, 28). Currently, the Andes restrict the geographic range of western species, leaving only a relatively narrow belt between the mountains and the Pacific Ocean (29).Finally, the genetic complexity of the unique adaptations observed in the bush dog (Speothos venaticus) and the maned wolf (Chrysocyon brachyurus), sister species with extraordinary morphological differences (30–36), has not been explored. The bush dog is the only obligate meat-eating (hypercarnivorous) canid in the Americas that survived the Late Pleistocene extinction (11, 36). It has a suite of dental and skeletal specializations that are linked to its ability to capture and process prey (37–39). These features include short robust legs with webbed feet to dig burrows for hunting and shelter, long bodies with short tails, a unique extension of the meat cutting blade in the upper fourth premolar (P4) and lower first molar (M1) teeth (a trenchant heel), and loss of molars which in other canids function to crush hard plant foods (36, 38–40). The maned wolf is the only large-bodied canid in South America to survive the Late Pleistocene megafaunal extinctions, which may reflect its ability to exploit a wide range of foods in the savanna-like Cerrado environment, including a large proportion of fruits in its diet (30, 31, 41–43). Furthermore, the maned wolf has the longest limbs among canids (Fig. 1) but is not a swift runner (31, 35), as its speed is limited by its unique racking gait characterized by lifting both feet on each side of the body simultaneously, facilitating movement through tall grassland (30, 44). Although certain aspects of the biology of bush dogs and maned wolves have been extensively studied (30–36), the genomic underpinnings of their extraordinary adaptations remain unknown.We investigated the evolutionary history of South American (SA) canids using newly generated whole-genome sequence data to assess phylogenetic relationships, evidence of interspecies gene flow, demographic history, and patterns of genomic diversity. To investigate adaptive evolution and genome variation in the maned wolf and bush dog, we generated de novo genome assemblies for both species and additionally sequenced four maned wolves and three bush dogs to characterize patterns of genetic diversity in the wild.