The gene tree delusion

Springer, Mark S.; Gatesy, John

doi:10.1016/j.ympev.2015.07.018

Cited by 277 publications

(258 citation statements)

References 101 publications

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“…Despite the keen interest in mammals, the evolutionary history of this clade has been and remains at the centre of heated scientific debates [4,5,[7][8][9][10][11][12]. In part, these controversies stem from the widespread occurrence of convergent morphological characters in mammals, which makes it difficult to tease apart homology and homoplasy in phylogenetic analyses that are solely based on these characters [4,9,13,14].…”

Section: Introductionmentioning

confidence: 99%

“…Notable exceptions include South American ungulates and glyptodonts, which have been positioned in the mammalian tree based on protein sequences of type I collagen [17] and complete mitogenomic DNA sequences [18], respectively. Even for molecular data, different data types require different phylogenetic models [14], each of which has its own limitations [10]. Whole genome analyses have promised to revolutionize our understanding of animal evolutionary history, but some claims for the robust resolution of difficult nodes with phylogenomic data are underpinned by problematic analyses and/or poor data [10,19,20].…”

Section: Introductionmentioning

confidence: 99%

“…Even for molecular data, different data types require different phylogenetic models [14], each of which has its own limitations [10]. Whole genome analyses have promised to revolutionize our understanding of animal evolutionary history, but some claims for the robust resolution of difficult nodes with phylogenomic data are underpinned by problematic analyses and/or poor data [10,19,20]. Despite these difficulties, there is consensus over the main topology [4][5][6] even though a few local polytomies are still unresolved (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Mammal madness: is the mammal tree of life not yet resolved?

Foley

Springer

Teeling

2016

Phil. Trans. R. Soc. B

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217

195

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One contribution of 15 to a discussion meeting issue 'Dating species divergences using rocks and clocks'. Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90-110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position and divergence time of the root of placental mammals, and certain 'hard nodes' such as the Laurasiatheria polytomy and Paenungulata that seem impossible to resolve. Here, we explore recent consensus and conflict among mammalian phylogenetic studies and explore the reasons for the remaining conflicts. The question of whether the mammal tree of life is or can be ever resolved is also addressed.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Mammal madness: is the mammal tree of life not yet resolved?

Foley

Springer

Teeling

2016

Phil. Trans. R. Soc. B

Self Cite

217

195

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show abstract

“…Thus, increasing fragment length would not challenge the standard MSC model, as long as each fragment is statistically independent. The observation that increasing sequence length decreases the probability of sampling sites with coincidental histories was criticized by Springer and Gatesy (2016) as a “full circle” return to the early stages of molecular phylogenetics, when DNA sequencing was technically challenging and expensive. Our empirical results can be used to evaluate the “full circle” criticism.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, Springer and Gatesy (2016) argued that for lineages as old as placental mammals, genomic segments free from intralocus recombination were limited to 12 bp. Thus, as MSC analyses frequently rely on loci encompassing thousands of base pairs (Song et al., 2012), lack of intralocus recombination was expected to be highly unlikely, a reason why a “concatalescence” analysis would frequently be performed, instead of the standard MSC.…”

Section: Introductionmentioning

confidence: 99%

Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages

Schrago

Mello

Pereira

et al. 2017

Ecology and Evolution

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Multispecies coalescent (MSC) theory assumes that gene trees inferred from individual loci are independent trials of the MSC process. As genes might be physically close in syntenic associations spanning along chromosome regions, these assumptions might be flawed in evolutionary lineages with substantial karyotypic shuffling. Neotropical primates (NP) represent an ideal case for assessing the performance of MSC methods in such scenarios because chromosome diploid number varies significantly in this lineage. To this end, we investigated the effect of sequence length on the theoretical expectations of MSC model, as well as the results of coalescent‐based tree inference methods. This was carried out by comparing NP with hominids, a lineage in which chromosome macrostructure has been stable for at least 15 million years. We found that departure from the MSC model in Neotropical primates decreased with smaller sequence fragments, where sites sharing the same evolutionary history were more frequently found than in longer fragments. This scenario probably resulted from extensive karyotypic rearrangement occurring during the radiation of NP, contrary to the comparatively stable chromosome evolution in hominids.

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Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

et al. 2018

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Premise of the StudyThe development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts.MethodsUsing 30 transcriptomes, we compared Hyb‐Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation‐ and coalescent‐based methods.ResultsHyb‐Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least flagged as paralogous. Y&S offered the most parsimony‐informative sites and putative orthologs. Target recovery averaged 93% across taxa. We optimized our targeted locus set based on a workflow designed to minimize paralog/ortholog conflation and thus present 423 loci for legume phylogenomics.ConclusionsMethods differed across criteria important for phylogenetic marker development. We recommend Hyb‐Seq as a method that may be useful for most phylogenomic projects. Our targeted locus set is a resource for future, community‐driven efforts to reconstruct the legume tree of life.

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The gene tree delusion

Cited by 277 publications

References 101 publications

Mammal madness: is the mammal tree of life not yet resolved?

Mammal madness: is the mammal tree of life not yet resolved?

Impact of long‐term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages

Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

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