Do Molecular Clocks Run at All? A Critique of Molecular Systematics

  title={Do Molecular Clocks Run at All? A Critique of Molecular Systematics},
  author={Jeffrey H Schwartz and Bruno Maresca},
  journal={Biological Theory},
Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between… 
Organismal Biology, Molecular Systematics, and Phylogenetic Reconstruction
DNA sequence data enjoys the singular position of being the arbiter of phylogenetic relationships; yet the justifications for this endeavor were based on studies of bacteria not multicellular organisms, which suggests that sequence similarity in this region reflects primitive retention (= nonchange.
Reflections on Systematics and Phylogenetic Reconstruction
I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline,
Systematics and Evolution
This chapter will be made to summarize the main aspects of these fields of inquiry, including their assumptions, and to suggest avenues of future inquiry that might bring these disciplines together to provide some better information about evolution.
Biogeography and the molecular dating game: a futile revival of phenetics?
In molecular dating, branch lengths are considered parameters that may be estimated by counting similari- ties and differences in DNA sequences, which might appear informative additions when imposed on a tree that is otherwise cladistic.
Evolution of human–ape relationships remains open for investigation
We demonstrate that much of the morphological and metrical data Lehtonen et al. (Journal of Biogeography, 2011, 38, 805–808) present in support of a closer relationship between humans and chimpanzees
Who is the closest extant cousin of humans? Total‐evidence approach to hominid phylogenetics via simultaneous optimization
The results supported the human–chimpanzee clade, without any phenotypical–molecular data conflict, as the same phylogeny emerged both from the total analysis and when the molecular and phenotypic data were analysed separately.
Phylogeny of Higher Taxa in Insecta: Finding Synapomorphies in the Extant Fauna and Separating Them from Homoplasies
The interpretations of higher phylogenies and evolutionary processes in Hexapoda are critically compared with those based on the evolution of organ systems, by using the groundplan method.
A Note On The Denisova Cave mtDNA Sequence
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation.
Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept
An alternative interpretation of the data presented on the Denisova fossil remains is advanced, concerned with the problem of contamination/degradation of the determined DNA sequenced and the claims for gene transfer among a number of Mid Pleistocene hominids.
Systematics and evolutionary biology: uneasy bedfellows? Sistemática y biología evolutiva: ¿compañeros incómodos?
The history of systematics and evolutionary biology demonstrates how greatly the "modern evolutionary synthesis" instrumentally prevented, rather than facilitated, the intellectual growth and


Molecular Systematics and Evolution
This entry will attempt to summarize the main aspects of these fields of inquiry, including their underlying assumptions, and suggest possible avenues for future research that might bring these disciplines together in light of new ways of thinking about evolution.
Evidence on human origins from haemoglobins of African apes
R rigorously determined α- and β-haemoglobin amino acid sequences not only of chimpanzee and Gorilla gorilla but also pygmy chimpanzee (Pan paniscus) are reported, which favour the explanation of decelerated evolution and point to selection preserving perfected haemoglobin molecules.
Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets.
  • M. Ruvolo
  • Biology
    Molecular biology and evolution
  • 1997
The multiple-locus test (Wu 1991), which evaluates hypotheses using gene tree-species tree mismatch probabilities in a likelihood ratio test, favors the phylogeny with a Homo-Pan clade and rejects the other alternatives with a P value of 0.002: the problem of hominoid phylogeny can be confidently considered solved.
Phylogenetic methods come of age: testing hypotheses in an evolutionary context.
The use of molecular phylogenies to examine evolutionary questions has become commonplace with the automation of DNA sequencing and the availability of efficient computer programs to perform
Recombination or mutation rate heterogeneity? Implications for Mitochondrial Eve.
The degree of single‐copy DNA divergence among the extant members of the Hominoidea is determined using the technique of DNA‐DNA hybridization using a member of the Old World monkeys (Cercopithecidae), the baboon.
Genetic evidence for complex speciation of humans and chimpanzees
This analysis shows that human–chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils and most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length.
Phylogeny and classification of birds based on the data of DNA-DNA hybridization
To reconstruct the phylogeny of a group of organisms it is necessary to define the monophyletic clusters of taxa, to determine the branching pattern of their divergences, and to place that pattern on the scale of absolute time.
Resolution of the African hominoid trichotomy by use of a mitochondrial gene sequence.
Comparisons of cytochrome oxidase subunit II gene sequences provide clear-cut evidence from the mitochondrial genome for the separation of the African ape trichotomy into two evolutionary lineages, one leading to gorillas and the other to humans and chimpanzees.
The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization
This work has compared the single-copy nuclear DNA sequences of the hominoid genera using DNA-DNA hybridization to produce a complete matrix of delta T50H values and shows that the branching sequence of the lineages was: Old World monkeys, gibbons, Orangutan, Gorilla, chimpanzees, and Man.