OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics

Ranwez, Vincent; Delsuc, Frédéric; Ranwez, Sylvie; Belkhir, Khalid; Tilak, Marie‐Ka; Douzery, Emmanuel J. P.

doi:10.1186/1471-2148-7-241

Cited by 116 publications

(122 citation statements)

References 73 publications

Supporting

Mentioning

118

Contrasting

Order By: Relevance

“…First, the choice of one to one orthologous exonic sequences ensures high mapping quality because of greater sequence conservation of exons compared to introns (Kerr et al, 2014;Ranwez et al, 2007). Moreover, the use of one to one orthologous sequences avoids the analytical com plexities introduced by duplicated genes (Maddison, 1997) and the occurrence of indels and greater sequence divergence that can pose substantial problems during multiple sequence alignment .…”

Section: Discussionmentioning

confidence: 99%

“…We used both supertree and supermatrix techniques (Delsuc et al, 2005). First, the concatenated alignment was analysed under two com monly used substitution models (GTR + r and GTR + r + 1), both with 100 bootstrap replications (Ranwez et at., 2007). Second, we selected 3570 one to one orthologous genes {thus combining the gene exons) with a minimum length of 500 bp.…”

Section: Phylogenomic Analysesmentioning

confidence: 99%

See 1 more Smart Citation

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs

Megens

Kraus

et al. 2016

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

a b s t r a c tPhylogenetic incongruence can be caused by analytical shortcomings or can be the result of biological processes, such as hybridization, incomplete lineage sorting and gene duplication. Differentiation between these causes of incongruence is essential to unravel complex speciation and diversification events. The phylogeny of the True Geese (tribe Anserini, Anatidae, Anseriformes) was, until now, con tentious, i.e., the phylogenetic relationships and the timing of divergence between the different goose species could not be fully resolved. We sequenced nineteen goose genomes (representing seventeen spe cies of which three subspecies of the Brent Goose, Branta bernicla) and used an exon based phylogenomic approach (41,736 exons, representing 5887 genes) to unravel the evolutionary history of this bird group. We thereby provide general guidance on the combination of whole genome evolutionary analyses and analytical tools for such cases where previous attempts to resolve the phylogenetic history of several taxa could not be unravelled. Identical topologies were obtained using either a concatenation (based upon an alignment of 6,630,626 base pairs) or a coalescent based consensus method. Two major lineages, corre sponding to the genera Anser and Branta, were strongly supported. Within the Branta lineage, the White cheeked Geese form a well supported sub lineage that is sister to the Red breasted Goose (Branta ruficol lis). In addition, two main clades of Anser species could be identified, the White Geese and the Grey Geese. The results from the consensus method suggest that the diversification of the genus Anser is heavily influ enced by rapid speciation and by hybridization, which may explain the failure of previous studies to resolve the phylogenetic relationships within this genus. The majority of speciation events took place in the late Pliocene and early Pleistocene (between 4 and 2 million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of tem perate grasslands. Our approach will be a fruitful strategy for resolving many other complex evolutionary histories at the level of genera, species, and subspecies.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Phylogenomic Analysesmentioning

confidence: 99%

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs

Megens

Kraus

et al. 2016

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

show abstract

“…The small mitochondrial dataset consists of 13 protein-coding genes, concatenated to yield an 11,763-bp supermatrix. The small nuclear dataset consists of 15 protein coding genes selected from the OrthoMam database (Ranwez et al, 2007). The 15 genes were selected with the goal of obtaining a dataset of nuclear markers with heterogeneous evolutionary rates.…”

Section: Datasets and Alignmentmentioning

confidence: 99%

Performance of genomic data sets on the estimation of the divergence time of New World and Old World anthropoids

Schrago¹,

Voloch²

2014

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. The origin of New World anthropoids has received renewed attention since the advent of molecular dating methods that relax the assumption of a strict molecular clock. However, the studies conducted to date have estimated the time of the separation of New World and Old World anthropoids at values as different as 70 and 22 Ma. With the aim of investigating the source of the discrepancies in the inferred ages, we have compared the performance of mitochondrial and nuclear markers in two pairs of datasets. We show that in the larger genomic samples, the dates of the separation of New and Old World anthropoids estimated from nuclear and mitochondrial data are significantly different.The precision of the estimates demonstrated that both markers rendered significantly different estimates. However, parametric estimates from the large nuclear dataset were highly cross-correlated. Cross-correlation of absolute divergence times and evolutionary rates was as great as -96%. Consequently, the age estimates from the large nuclear data were not reproducible, because Markov chains were unable to reach the same parametric values independently, even with the adoption of additional information from calibration priors. Thus, because branch length decomposition was not achieved, a comparison of the genomic age estimates from nuclear and mitochondrial datasets was statistically impractical. We demonstrate the importance of examining the output of Markov chain Monte Carlo analyses for correlation between rate and time in studies that use phylogenomic datasets to examine the chronological scales of primate evolution.

show abstract

“…First, the choice of one-to-one orthologous exonic sequences ensures high mapping quality because of greater sequence conservation of exons compared to introns (Ranwez et al, 2007, Kerr et al, 2014 Moreover, the use of one-to-one orthologous sequences avoids the analytical complexities introduced by duplicated genes (Maddison, 1997) and the occurrence of indels and greater sequence divergence that can pose substantial problems during multiple sequence alignment . Second, the genome-wide set of thousands of genes enabled us to deduce with high statistical power the species tree despite potentially high levels of phylogenetic incongruence caused by incomplete lineage sorting and/or hybridization.…”

Section: Phylogenetic Relationships)mentioning

confidence: 99%

“…We used both supertree and supermatrix techniques (Delsuc et al, 2005). First, the concatenated alignment was analysed under two commonly used substitution models (GTR + Γ and GTR + Γ + I), both with 100 bootstrap replications (Ranwez et al, 2007). Second, we selected 3,570 one-to-one orthologous genes (thus combining the gene exons) with a minimum length of 500 bp.…”

Section: Phylogenomic Analysesmentioning

confidence: 99%

Crossing species boundaries : the hybrid histories of the true geese

Ottenburghs¹

View full text Add to dashboard Cite

. Crossing Species Boundaries: The Hybrid Histories of the True Geese. PhD thesis, Wageningen University, the Netherlands. Hybridization, the interbreeding of different species, is a common phenomenon in birds: about 16% of bird species is known to have hybridized with at least one other species. Numerous avian hybrid zones have been studied from a morphological or genetic perspective, often documenting the interspecific exchange of genetic material by hybridization and backcrossing (i.e. introgression). The incidence of hybridization varies among bird orders with the Anseriformes (waterfowl: ducks, geese and swans) showing the highest propensity to hybridize. In this thesis, I provide a genomic perspective on the role of hybridization in the evolutionary history of one particular anseriform tribe, the Anserini or "True Geese", which comprises 17 species divided over two genera: Anser and Branta . The diversification of this bird group took place in the late Pliocene and the early Pleistocene (between four and two million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of temperate grasslands. Most species show a steady population increase during this period, followed by population subdivision during the Last Glacial Maximum about 110,000 to 12,000 years ago. The combination of large effective population sizes and occasional range shifts facilitated contact between the diverging goose species, resulting in high levels of interspecific gene flow. Introgressive hybridization might have enabled these goose populations to quickly adapt to changing environments by transferring of advantageous alleles across species boundaries, increasing standing genetic variation or expanding phenotypic variation of certain traits (e.g., beak morphology). Hybridization seems to be a common and integral component in the evolution and diversification of geese. The pervasiveness of rapid speciation and hybridization in geese complicates the attempt to capture their evolutionary history in a phylogenetic tree, therefore I advocate a phylogenetic network approach. Indeed, trying to capture the complex diversification of the True Geese in a branching tree can be regarded as a wild goose chase. Abstract TABLE OF CONTENTS

show abstract

OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics

Cited by 116 publications

References 73 publications

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Performance of genomic data sets on the estimation of the divergence time of New World and Old World anthropoids

Crossing species boundaries : the hybrid histories of the true geese

Contact Info

Product

Resources

About