Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans
2015/11/09 by Gillian C. Gibb, Fabien L. Condamine, Melanie Kuch +5 · 1 voice · 37 citations
Earth and Planetary Sciences · Biochemistry, Genetics and Molecular Biology · Agricultural and Biological Sciences · #Evolution and Paleontology Studies #Genomics and Phylogenetic Studies #Bat Biology and Ecology Studies
paper · pdf · doi:10.1093/molbev/msv250
Abstract
Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.
Cited by
- From Rigid Order to Radical Variation: Mitogenome Evolution in the Main Lineages of a Lesser-Known Animal Phylum (Gastrotricha)
- Ontogeny and associated changes of the extinct sloth Simomylodon uccasamamensis (Xenarthra, Mylodontidae) from the Pliocene of the eastern Puna, Argentina
- Nine biomes and nine challenges for the conservation genetics of Neotropical species, the case of the vulnerable giant anteater (Myrmecophaga tridactyla)
- The presence of an atavistic caniniform alveolus in Nothrotherium maquinense (Xenarthra, Folivora, Nothrotheriidae)
- Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models
- Dental enamel structure in long-nosed armadillos (Xenarthra:Dasypus) and its evolutionary implications
- Morphological disparity and evolutionary rates of cranial and postcranial characters in sloths (Mammalia, Pilosa, Folivora)
- The emergence and demise of giant sloths
- Pseudogenes document protracted parallel regression of oral anatomy in myrmecophagous mammals
- Long-read sequencing and genome assembly of natural history collection samples and challenging specimens
- Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution
- Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield
- Genome-Wide Screening of Retroviral Envelope Genes in the Nine-Banded Armadillo (Dasypus novemcinctus, Xenarthra) Reveals an Unfixed Chimeric Endogenous Betaretrovirus Using the ASCT2 Receptor. [europepmc]
- Global biogeography since Pangaea. [europepmc]
- The hidden anatomy of paranasal sinuses reveals biogeographically distinct morphotypes in the nine-banded armadillo ( Dasypus novemcinctus ). [europepmc]
- Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus ). [europepmc]
- Trabecular architecture in the forelimb epiphyses of extant xenarthrans (Mammalia). [europepmc]
- Cranial osteology of the pampathere Holmesina floridanus (Xenarthra: Cingulata; Blancan NALMA), including a description of an isolated petrosal bone. [europepmc]
- Phylogeography of screaming hairy armadillo Chaetophractus vellerosus: Successive disjunctions and extinctions due to cyclical climatic changes in southern South America. [europepmc]
- Taxonomic revision of the long-nosed armadillos, Genus Dasypus Linnaeus, 1758 (Mammalia, Cingulata). [europepmc]
- Evolutionary adaptation to aquatic lifestyle in extinct sloths can lead to systemic alteration of bone structure. [europepmc]
- Resolving the phylogenetic position of Darwin's extinct ground sloth ( Mylodon darwinii ) using mitogenomic and nuclear exon data. [europepmc]
- Ontogenetic changes in the long bone microstructure in the nine-banded armadillo (Dasypus novemcinctus). [europepmc]
- A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues. [europepmc]
- Comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals. [europepmc]
- Identification and characterization of satellite DNAs in two-toed sloths of the genus Choloepus (Megalonychidae, Xenarthra). [europepmc]
- Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms. [europepmc]
- Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. [europepmc]
- Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. [europepmc]
- Comparative mitogenome phylogeography of two anteater genera ( Tamandua and Myrmecophaga ; Myrmecophagidae, Xenarthra): Evidence of discrepant evolutionary traits. [europepmc]
- Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals. [europepmc]
- Diversification dynamics in the Neotropics through time, clades, and biogeographic regions. [europepmc]
- Xenarthrans of the collection of Santiago Roth from the Pampean Region of Argentina (Pleistocene), in Zurich, Switzerland. [europepmc]
- Macroecological diversification of ants is linked to angiosperm evolution. [europepmc]
- Long-read sequencing and genome assembly of natural history collection samples and challenging specimens. [europepmc]
- From Rigid Order to Radical Variation: Mitogenome Evolution in the Main Lineages of a Lesser-Known Animal Phylum (Gastrotricha). [europepmc]
- Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution. [europepmc]
Discussions
Related