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

Abstract

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.

Lepidoptera genomics based on 88 chromosomal reference sequences informs population genetic parameters for conservation

“…Comparing the patterns of variation in the genomes of species of different conservation concerns uncovers the evolutionary history, demography, and molecular adaptations of species 44 . It supports the prioritisation of species for future targeted population genomics, which is particularly relevant for species that lack longterm monitoring data.…”

Different, but the same: Inferring the hunting behaviour of the hypercarnivorous bush dog (Speothos venaticus) through finite element analysis

“…It is known by the Matse people of north‐eastern Peru that the bush dog actively hunts the long‐nosed armadillo ( Dasypus kappleri ) by entering the armadillo's burrow, capturing it in the tunnels and dragging it to the entrance of the burrow, where it is finally consumed (Fleck & Voss, 2016). Some authors suggest that its interdigital membranes are also helpful while digging (Chavez et al, 2022), and its robust forelimbs are distinct to the slender bones of cursorial Carnivora, being more similar—although not as robust—to those of the Canadian river otter ( Lontra canadensis ) and European badger ( Meles meles ), mustelids of aquatic and burrowing habits respectively (Martín‐Serra et al, 2014). These behaviour and anatomic adaptations could help the bush dogs since, presumably, prey movements become reduced in the water and in narrow space, and also may be related to the bush dog's cranium being less suited to deal with lateral movements, as seen in the head shaking scenarios (Figure 5).…”

“…Cerdocyonina is a lineage of South‐American endemic canids that include some of the least‐known extant canid species (Figure 1, Chavez et al, 2022; DeMatteo & Loiselle, 2008; Pitman & Beisiegel, 2013; Tensen, 2018). This group comprises generalist fox‐like morphotypes ( Cerdocyon , Atelocynus and Lycalopex ), as well as highly specialised species such as the maned wolf ( Chrysocyon brachyurus ) and the bush dog ( Speothos venaticus , Chavez et al, 2022; Lindblad‐Toh et al, 2005; Segura et al, 2021; Wozencraft, 2005). Most Cerdocyonina are mesocarnivores (i.e.…”

Sarcocystis spp. of New and Old World Camelids: Ancient Origin, Present Challenges

“…only around 5–10 kya, other canids must have previously fulfilled this role after the arrival of camelids to South America 3.9 to 3.5 mya; later, a host shift to C. familiaris must have occurred. Extant autochthonous canids whose habitats coincide with those of SACs in the Andean regions include the Culpeo fox ( Lycalopex culpaeus ), the South American gray fox ( Lycalopex griseus ), and, with more limited distribution, the Sechuran fox or Peruvian desert fox ( Lycalopex sechurae ) and Darwin’s fox ( Lycalopex fulvipes ) [ 88 ]. A role for these canids as definitive hosts of S. aucheniae and/or S. masoni , either by predating or—more likely—scavenging on dead SAC carcasses can be hypothesized but awaits experimental confirmation.…”