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Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics.

ABSTRACT: The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve, and 11 of the 15 possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used a high-throughput assay with 54,693 SNP loci developed for Bos taurus taurus to rapidly genotype 678 individuals representing 61 Pecoran species. We produced a highly resolved phylogeny for this diverse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a method to amplify and screen genomic information from extinct species, and place Bison priscus within the Bovidae. The quality of genotype calls and the placement of samples within a well-supported phylogeny may provide an important test for validating the fidelity and integrity of ancient samples. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.

SUBMITTER: Decker JE

PROVIDER: S-EPMC2765454 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Snout shape is a prominent aspect of herbivore feeding ecology, interacting with both forage selectivity and intake rate. Previous investigations have suggested ruminant feeding styles can be discriminated via snout shape, with grazing and browsing species characterised by 'blunt' and 'pointed' snouts respectively, often with specification of an 'intermediate' sub-grouping to represent ambiguous feeding styles and/or morphologies. Snout shape morphology is analysed here using a geometric morphometric approach to compare the two-dimensional profiles of the premaxilla in ventral aspect for a large sample of modern ruminant species, for which feeding modes are known from secondary criteria. Results suggest that, when browsing and grazing ruminants are classified ecologically based on a range of feeding style indicators, they cannot be discriminated unambiguously on the basis of snout profile shape alone. Profile shapes in our sample form a continuum with substantial overlap between groupings and a diverse range of morphologies. Nevertheless, we obtained an 83.8 percent ratio of correct post hoc feeding style categorisations based on the proximity of projected profile shapes to group centroids in the discriminant space. Accordingly, this procedure for identifying species whose feeding strategy is 'unknown' can be used with a reasonable degree of confidence, especially if backed-up by additional information. Based on these results we also refine the definitions of snout shape varieties, taking advantage of the descriptive power that geometric morphometrics offers to characterize the morphological disparities observed. The shape variance exhibited by both browsing and grazing ruminants corresponds strongly to body mass, providing further evidence for an interaction between snout shape, feeding style, and body size evolution. Finally, by exploring the role of phylogenetic similarity in snout shape, we find a slight increase in successful categorisation when repeating the analysis with phylogenetic control on the geometric profiles.

Project description:Evolutionary studies of insular biotas are based mainly on extant taxa, although such biotas represent artificial subsets of original faunas because of human-caused extinctions of indigenous species augmented by introduced exotic taxa. This makes it difficult to obtain a full understanding of the history of ecological interactions between extant sympatric species. Morphological bill variation of Fringilla coelebs and F. teydea (common and blue chaffinches) has been previously studied in the North Atlantic Macaronesian archipelagos. Character displacement between both species has been argued to explain bill sizes in sympatry. However, this explanation is incomplete, as similar patterns of bill size have been recorded in F. coelebs populations from islands with and without F. teydea.The discovery of a new extinct species in Tenerife (Canary Islands), here named Carduelis aurelioi n. sp. (slender-billed greenfinch), provides the opportunity to study ancient ecological interactions among Macaronesian finches. To help understand the evolutionary histories of forest granivores in space and time, we have performed a multidisciplinary study combining: (1) morphological analyses and radiocarbon dating (11,460±60 yr BP) of the new taxon and, (2) molecular divergence among the extant finch species and populations in order to infer colonization times (1.99 and 1.09 My for F. teydea and F. coelebs respectively).C. aurelioi, F. coelebs and F. teydea co-habited in Tenerife for at least one million years. The unique anatomical trends of the new species, namely chaffinch-like beak and modified hind and forelimbs, reveal that there was a process of divergence of resource competition traits among the three sympatric finches. The results of our study, combined with the presence of more extinct greenfinches in other Macaronesian islands with significant variation in their beak sizes, suggests that the character displacement has influenced patterns of divergence in bill size and shape on other Macaronesian islands as well.

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Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics.

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