Ecological diversification and biogeography in the Neogene: Evolution of a major lineage of American and Caribbean rodents (Caviomorpha, Octodontoidea)

Abstract

A major topic in evolutionary biology concerns the process of biological diversification. The cosmopolitan order Rodentia is the most diverse mammalian radiation with ca. 2300 living species, or about 40% of all mammals. The Caviomorpha, best known from the domesticated guinea pig (Cavia), was the first rodent lineage to reach South America. Their Eocene origin from Africa is supported by both molecular and paleontological data sets. Caviomorphs have since radiated to 244 modern species in the Americas and Caribbean, spanning three orders of magnitude in body size (i.e., ~60 g to ~60 kg). The superfamily Octodontoidea (186 species) collectively exploits most ecological niches used by rodents, from tree-dwelling to burrowing, rock-dwelling, terrestrial, and even semi-aquatic forms. Reconstructing the timing and patterns of this evolutionary diversification has been problematic, however, due to convergent morphologies, incomplete fossils, and sparse sampling of species in molecular phylogenies. The goals of this dissertation were to (i) establish a temporal and phylogenetic framework for this lineage consistent with fossil and molecular data, and (ii) use it to investigate ecological and geographic drivers of diversification over the last 23 million years (Neogene – Recent).

Molecular phylogenetic analyses were conducted across all 54 living genera (and 68% of species) in Caviomorpha plus related rodents in Africa and Asia for two mitochondrial (cyt-b and 12S rRNA) and three nuclear genes (GHR, vWF, and RAG1). Clade divergence times were estimated using a relaxed molecular clock and 22 fossil calibrations. The timetree supports the divergence of Caviomorpha from Phiomorpha (Africa) in the Middle Eocene ~42 Ma, presumably via over-water dispersal to South America. That clade + African and Asian porcupines is strongly supported as crown Hystricognathi with an ~45 Ma age. Within Phiomorpha, the ~31 Ma divergence of the naked mole-rat (Heterocephalus) from all other mole-rats argues for recognition of this group as Bathyergoidea, containing the families Heterocephalidae and Bathyergidae. Within Caviomorpha, the four traditional superfamilies were recovered with ~32 Ma stem divergences as Cavioidea + Erethizontoidea and Chinchilloidea + Octodontoidea. Five families were united in Octodontoidea, with Abrocomidae (chinchilla rats) sister to two family dyads: Octodontidae (degus and viscacha rats) + Ctenomyidae (tuco-tucos) and Echimyidae (spiny rats, tree rats, and the nutria) + Capromyidae (hutias). Although the five genera of capromyids form a robustly monophyletic group, they were recovered as the uncertain sister to a group of Brazilian echimyids, possibly rendering Echimyidae paraphyletic.

Processes of geographic diversification were reconstructed using the timetree, geographic ranges for extant caviomorphs, and regions of endemism. By the beginning of the Neogene, each main lineage of Octodontoidea had diverged from an ancestor most likely distributed in the Southern Andes/Patagonia. With the onset of more arid climates in southern South America ~18 Ma, the crown radiations of both family dyads had begun. Ensuing divergences in space and ecology resulted in a southern, arid-adapted clade (Octodontidae-Ctenomyidae, 76 species) and a northern, mesic-adapted clade (Echimyidae-Capromyidae, 102 species). Rates of species diversification were dramatically different among these clades, with a long stem leading to the last ~5 Ma of rapid radiation in Ctenomyidae, versus at least 18 lineages present by 10 Ma in Echimyidae-Capromyidae. The best-fitting processes for these patterns were positive diversity dependence (likely due to high species turnover) in Octodontidae-Ctenomyidae, and either decreasing diversity dependence or constant rates in Echimyidae-Capromyidae. The geo-climatic differentiation of northern and southern South America during the Neogene may have driven the disparate divergence processes for these rodent clades. The uplift of montane Andean habitats is implicated in both the aridification of southern climates and in the northern radiation of Echimyidae, with at least four transitions found in their phylogeny between the lowland Amazon and highland Andes. A survey of 86 other animal lineages reinforces that finding, and suggests that both directions of transition were common after ~7.5 Ma.

Processes of ecological diversification were investigated to test for signatures of adaptive radiation throughout the timetree. Body masses and ecological life modes were mapped on the timetree for all species and used for modeling body-size disparification. Different evolutionary processes again characterized Octodontoidea’s northern and southern clades. In Ctenomyidae, rates of body-size disparification accelerated in step with species diversification, and in accord with their modern species’ 10-fold variation in body mass. In contrast, analyses of Echimyidae-Capromyidae showed initially high and then declining rates of disparification. Among reconstructed life modes, multi-optimum Ornstein-Uhlenbeck models were favored over constant rate (Brownian motion) models. Rodents in different life modes appear to occupy different regions of morphospace and, presumably, ecospace. Burrowing rodents were modeled as having a significantly smaller and less variable optimum size than tree-dwelling or terrestrial rodents, suggesting that subterranean living may impose size constraints. In the context of Simpson’s adaptive zones, Ctenomyidae is confined to the single zone of burrowing while Echimyidae-Capromyidae occupies at least two (burrowing and tree-dwelling). Hence, even though Ctenomyidae is both diverse and disparate it does not appear to constitute an adaptive radiation. Echimyidae-Capromyidae is a candidate for an old adaptive radiation that has persisted after saturating available niches. In both cases, greater integration of phylogenetic and geographic information from fossils is expected to improve our understanding of these radiations.