Mitogenomic relationships of placental mammals and molecular estimates of their divergences

Árnason, Úlfur; Adegoke, Joseph A.; Gullberg, Anette; Harley, Eric H.; Janke, Axel; Kullberg, Morgan

doi:10.1016/j.gene.2008.05.024

Cited by 150 publications

(158 citation statements)

References 85 publications

(159 reference statements)

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“…In addition, our study confirms Scandentia as the sister group of Primates, providing a context to study early character and genome evolution in the lineages leading to primates and humans (36). Finally, our data support Perissodactyla (odd-toed ungulates), Carnivora, and Cetartiodactyla (including eventoed ungulates and Cetacea) as a monophyletic clade within Laurasiatheria (37)(38)(39)(40). Differing from the traditional view, however, we find that odd-toed ungulates are more closely related to carnivores than to even-toed ungulates (38)(39)(40), suggesting an emergence of carnivores from within a paraphyletic ungulate clade.…”

Section: Discussionsupporting

confidence: 74%

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Song

Liu

Edwards

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

429

774

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The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both Bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.

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Section: Discussionsupporting

confidence: 74%

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Song

Liu

Edwards

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

429

774

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“…Thus, it appears that the common ancestor of the Macroscelididae, Chrysochloridae and Hyracoidea may have had this trait. While this concept is supported for the Macroscelididae and Chrysochloridae, to the exclusion of the Tenrecidea, due to the closer relationship of the Macroscelididae and Chrysochloridae, the occurrence of this trait in the Hyracoidea indicates, based on current understandings of the phylogenetic relationships of the Afrotheria (Arnason et al, 2008;Asher et al, 2009), that either this character evolved twice, or was lost in the Tenrecidea. Further comparative work on the anatomy of the locus coeruleus in other members of the Afrotheria will resolve this problem.…”

Section: Differences In the Catecholaminergic Systems And Phylogenetimentioning

confidence: 99%

“…van Dijk et al, 2001;Arnason et al, 2008;Hallström and Janke, 2008;Prasad et al, 2008;Asher et al, 2010;Dumbacher et al, 2012;McCormack et al, 2012). Within the Afrotheria are species that are fully aquatic (such as manatees and dugongs), extremely large (elephants), fossorial (golden moles), semi-aquatic (otter shrews), insectivorous (aardvarks, elephants shrews and tenrecs) and omnivorous (hyraxes).…”

Section: Introductionmentioning

confidence: 99%

Nuclear organisation of some immunohistochemically identifiable neural systems in three Afrotherian species—Potomogale velox, Amblysomus hottentotus and Petrodromus tetradactylus

Calvey

Patzke

Kaswera

et al. 2013

Journal of Chemical Neuroanatomy

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Paul.Manger@wits.ac.za 2 Highlights  The organisation of four neural systems is described in the brains of three Afrotherians not previously studied  These systems are organised in a similar manner to other mammals.  There are features that reflect both phylogenetic and functional signals in the evolution of these neural systems.  The golden mole appears to be a "hyper-cholinergic" mammal, possessing cholinergic neurons in novel regions of the brain. AbstractThe present study describes the organization of the cholinergic, catecholaminergic, serotonergic and orexinergic (hypocretinergic) neurons in the brains of the giant otter shrew, the Hottentot golden mole and the four-toed sengi, three members of the mammalian super orderAfrotheria. The aim of the present study was to investigate the possible differences in the nuclear complement of these neural systems in comparison to previous studies on other Afrotheria species and other mammalian species. Brains of the golden mole, sengi and giant otter shrew were coronally sectioned and immunohistochemically stained with antibodies against cholineacetyl-transferase, tyrosine hydroxylase, serotonin and orexin-A. The majority of nuclei revealed in the current study were similar between the species investigated, to other Afrotherian species investigated, and to other mammals, but certain differences in the nuclear complement highlighted phylogenetic interrelationships. The golden mole was seen to have cholinergic interneurons in the cerebral cortex, hippocampus, olfactory bulb and amygdala. The four-toed sengi had cholinergic neurons in both colliculi and in the cochlear nucleus, but lacked the catecholaminergic A15d group in the hypothalamus. In both the golden mole and the four-toed sengi, the locus coeruleus (A6d group) was made up of few neurons. The golden mole also exhibited an unusual foreshortening of the brain, such that a major kink in the brainstem was evident. The results of this study, framed in a phylogenetic context, appear to indicate that the golden mole and four-toed sengi share a more recent common ancestor that diverged from the tenrec lineage early in the phylogenetic history of the Afrotherians.

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“…Recently, complete mitochondrial genome sequences (usually 16–17 kbp among vertebrate species) have proven useful in clarifying phylogenetic relationships among species (Arnason et al., 2008; Cooper et al., 2001; Coulson, Marshall, Pepin, & Carr, 2006; Horai, Hayasaka, Kondo, Tsugane, & Takahata, 1995; Inoue, Miya, Tsukamoto, & Nishida, 2001; Miya, Kawaguchi, & Nishida, 2001; Miya et al., 2003). Following extensive use in human population and evolutionary genetics (Horai et al., 1995; Ingman, Kaessmann, Pääbo, & Gyllensten, 2000; Mishmar et al., 2003; Pope, Carr, Smith, & Marshall, 2011; Tanaka et al., 2004), increasing use has been made in intraspecific studies of fish (Carr & Marshall, 2008a; Feutry et al., 2014; Teacher, André, Merilä, & Wheat, 2012) and other mammals (Carr et al., 2015; Knaus, Cronn, Liston, Pilgrim, & Schwartz, 2011; Stone et al., 2010).…”

Section: Introductionmentioning

confidence: 99%

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Lait

Marshall

Carr

2018

Ecology and Evolution

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The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High‐resolution, whole‐genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans‐Atlantic comparisons (ΦST = .029–.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000–.060) or defined management stocks (ΦST = .000–.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans‐Atlantic phylogeography versus absence of such structure within various partitions of trans‐Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near‐identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153–.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200–250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

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Mitogenomic relationships of placental mammals and molecular estimates of their divergences

Cited by 150 publications

References 85 publications

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

Nuclear organisation of some immunohistochemically identifiable neural systems in three Afrotherian species—Potomogale velox, Amblysomus hottentotus and Petrodromus tetradactylus

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

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