How reticulated are species?

Mallet, James; Besansky, Nora J.; Hahn, Matthew W.

doi:10.1002/bies.201500149

Cited by 515 publications

(486 citation statements)

References 139 publications

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“…Horizontal transfer (reticulation) is much more common in nature than realized twenty years ago (see a nice summary by Mallet, Besansky, et al 2016). Despite having been presented as such (e.g., Wheeler and Platnick 2000), reticulation is not just a problem for the species level; clades at all levels can be subject to horizontal transfer.…”

Section: Capturing the Snarcmentioning

confidence: 99%

“…Horizontal genetic transfer can occur in a number of ways, summarized by (Soucy, Huang, et al 2015). However, it is notable that this usually offers a different phylogeny and recovers different taxa for the gene tree, not the taxon tree (Degnan and Rosenberg 2009 people have made for a long time between homology and homoplasy (Mallet, Besansky, et al 2016;Nixon and Carpenter 2011); in fact, horizontal gene transfer is best viewed as a type of homoplasy.…”

Section: Capturing the Snarcmentioning

confidence: 99%

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The Hunting of the SNaRC: A Snarky Solution to the Species Problem

Mishler¹,

Wilkins²

2018

Philosophy, Theory, and Practice in Biology

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We argue that the logical outcome of the cladistics revolution in biological systematics, and the move towards rankless phylogenetic classification of nested monophyletic groups as formalized in the PhyloCode, is to eliminate the species rank along with all the others and simply name clades. We propose that the lowest level of formally named clade be the SNaRC, the Smallest Named and Registered Clade. The SNaRC is an epistemic level in the classification, not an ontic one. Naming stops at that level because there is no currently acceptable evidence for clades within it, not because no smaller clades exist. Later, included clades may be named. They would then become the SNaRCs, while the original SNaRC would keep its original name. We argue that all theoretical tasks of biology, in evolution and ecology, as well as practical tasks such as conservation assessment, are better approached using this rankless phylogenetic approach.

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Section: Capturing the Snarcmentioning

confidence: 99%

Section: Capturing the Snarcmentioning

confidence: 99%

The Hunting of the SNaRC: A Snarky Solution to the Species Problem

Mishler¹,

Wilkins²

2018

Philosophy, Theory, and Practice in Biology

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“…The question of whether a "tree of life" exists has been discussed for decades, [7][8][9][10] and the recent publication of genome level phylogenies across many taxa brings enormous quantities of empirical data to bear on this question. These data demonstrate that a single genome often contains regions with divergent evolutionary histories.…”

Section: A Tree Of Life Is Not the Only Modelmentioning

confidence: 99%

“…And indeed, using this tree-like framework to test alternative hypotheses is essential to the practice of biology. [18] When Mallet et al [10] argue that "species tree signal. .…”

Section: A Tree Of Life Model Is Usefulmentioning

confidence: 99%

How and Why to Build a Unified Tree of Life

et al. 2017

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Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow‐up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

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“…Furthermore, there is growing evidence that archaic introgression occurred also within Africa (Labuda et al, 2000;Hammer et al, 2011;Lachance et al, 2012;Hsieh et al, 2016;Xu et al, 2017; Zanolli et al, 2017), raising the exciting possibility that other unknown archaic groups may have contributed to human genetic diversity. Therefore, recent work suggests that apparently distinct species can exchange the genetic material along their evolutionary history (Mallet et al, 2016). The biological implications of such introgression, including their consequences on modern human health is reviewed in the following sections.…”

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confidence: 99%

Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Dolgova

Lao

2018

Preprint

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The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered.It is currently known that AMH introgressed with archaic hominins once they left the African continent. Current out of African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.Keywords: archaic introgression, fitness, natural selection, Neanderthal, Denisova, anatomically modern humans. Peer-reviewed version available at Genes 2018, 9, 358; doi:10.3390/genes9070358 2 Widespread interbreeding between homininsThe demographic history of anatomically modern humans (AMH) is complex, and involves a large number of migrations, genetic admixtures and introgressions, population extinctions and genetic adaptations, which overlap both in time and in space (see Figure 1). Due to this complexity, the evolutionary history of humankind is still far from being fully understood (Nielsen et al., 2017). During the last 30 years, the most accepted demographic scenario for explaining recent evolution of AMH has been the Out of Africa model (OOA). According to this model, AMH evolved in Africa around 100-200 thousands years ago (kya) in East Africa and migrated to the rest of the world. Classical "pure" OOA assumes that admixture with other archaic populations such as Neanderthals or Denisovans, present at the time of the rise of AMH, either did not occur or was negligible (Lalueza-Fox & Gilbert, 2011). Figure 1. Family tree of the four groups of early humans living in Eurasia 50,000 years ago and the inferred gene flow between the groups due to interbreeding (based on Prüfer et al., 2014;Mondal et al., 2016;Hsieh et al., 2016; Medina-Gomez et al., 2017). The direction and estimated magnitude of inferred gene flow events are shown. Branch lengths and timing of gene flows are not scaled. The dashed line indicates that it is uncertain whether Denisovan gene flow into modern humans in mainland Asia occurred directly or via Oceania. Light violet color indicates introgression events from unknown archaic populations (Ghost).However, genomic studies of ancient DNA have revealed that AMH interbred with other hominid lineages, such as Neanderthals and Denisovans, present in Eurasia up to ∼30,000-50,000 years ago Quach & Quintana-Murci, 2017;Vattathil & Akey, 2015 New studies based on current genetic diversity are suggesting that the events of archaic introgression in AMH did occur out of Africa with other hidden "ghost" archaic populations (Mondal et al., 2016). Furthermore, there i...

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How reticulated are species?

Cited by 515 publications

References 139 publications

The Hunting of the SNaRC: A Snarky Solution to the Species Problem

The Hunting of the SNaRC: A Snarky Solution to the Species Problem

How and Why to Build a Unified Tree of Life

Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

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