The meaning of Neandertal skeletal morphology

Weaver, Timothy D.

doi:10.1073/pnas.0903864106

Cited by 125 publications

(68 citation statements)

References 73 publications

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“…It seems obvious that many relevant evolutionary processes took place between these two dates, perhaps related to dramatic climatic events and triggered by the action of genetic drift [64]. Moreover, it is not clear yet whether Neanderthals from other geographical areas or time periods are genetically similar to the ones that have already been analysed.…”

Section: Super-archaic Dnamentioning

confidence: 99%

“…Moreover, it is not clear yet whether Neanderthals from other geographical areas or time periods are genetically similar to the ones that have already been analysed. While there are clearly differences between early and late members of the Neanderthal lineage, opinions vary over the unity of European and Asian varieties of this hominin group [64,65]. It will be interesting to address how Neanderthals from different time points related to each other and to what extent climatic conditions or other factors contributed to shape their genetic diversity through adaptation and also demographic reductions and expansions.…”

Section: Super-archaic Dnamentioning

confidence: 99%

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Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

Sánchez-Quinto

Lalueza-Fox

2015

Phil. Trans. R. Soc. B

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Nearly two decades since the first retrieval of Neanderthal DNA, recent advances in next-generation sequencing technologies have allowed the generation of high-coverage genomes from two archaic hominins, a Neanderthal and a Denisovan, as well as a complete mitochondrial genome from remains which probably represent early members of the Neanderthal lineage. This genomic information, coupled with diversity exome data from several Neanderthal specimens is shedding new light on evolutionary processes such as the genetic basis of Neanderthal and modern human-specific adaptations-including morphological and behavioural traits-as well as the extent and nature of the admixture events between them. An emerging picture is that Neanderthals had a long-term small population size, lived in small and isolated groups and probably practised inbreeding at times. Deleterious genetic effects associated with these demographic factors could have played a role in their extinction. The analysis of DNA from further remains making use of new large-scale hybridization-capture-based methods as well as of new approaches to discriminate contaminant DNA sequences will provide genetic information in spatial and temporal scales that could help clarify the Neanderthal's-and our very own-evolutionary history.

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Section: Super-archaic Dnamentioning

confidence: 99%

Section: Super-archaic Dnamentioning

confidence: 99%

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

Sánchez-Quinto

Lalueza-Fox

2015

Phil. Trans. R. Soc. B

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“…Modern humans differ from their closest extinct relatives, Neandertals, in several aspects, including skeletal and skull morphology (Weaver 2009), and may also differ in other traits that are not preserved in the archeological record (Varki et al 2008;Laland et al 2010). Natural selection may have played a role in fixing these traits on the modern human lineage.…”

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confidence: 99%

Detecting ancient positive selection in humans using extended lineage sorting

et al. 2017

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Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set presentday humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation. Regions that are unusually long indicate the presence of lineages that reached fixation in the human population faster than expected under neutral evolution. Using simulations, we show that the method is able to detect ancient events of positive selection and that it can differentiate those from background selection. Applying our method to the 1000 Genomes data set, we find evidence for ancient selective sweeps favoring regulatory changes and present a list of genomic regions that are predicted to underlie positively selected human specific traits.[Supplemental material is available for this article.]Modern humans differ from their closest extinct relatives, Neandertals, in several aspects, including skeletal and skull morphology (Weaver 2009), and may also differ in other traits that are not preserved in the archeological record (Varki et al. 2008;Laland et al. 2010). Natural selection may have played a role in fixing these traits on the modern human lineage. However, the selection events driving the fixation would have been restricted to a specific timeframe, extending from the split between archaic and modern humans ca. 650,000 yr ago to the split of modern human populations from each other around 100,000 yr ago . While methods exist that can be used to scan the genome for the remnants of past or ongoing positive selection (Nielsen et al. 2007; Pybus and Shapiro 2009), current methods have limited power to detect positive selection on the human lineage that acted during this older timeframe (see Sabeti et al. 2006 for a review on detection methods and their timeframes): an unusually high ratio of functional changes to nonfunctional changes, such as the d N /d S test, requires millions of years and often multiple events of selection to generate detectable signals (Kryazhimskiy and Plotkin 2008), while unusual patterns of genetic diversity between individuals and populations (e.g., extended homozygosity, Tajima's D, F ST ) are most powerful during the selective sweep or shortly after (Sabeti et al. 2006;Oleksyk et al. 2010). A favorable substitution is not expected to leave a mark on linked neutral variation beyond 250,000 yr in humans (Przeworski 2002(Przeworski , 2003.The genome sequencing of archaic humans (Neandertals and Denisovans) to high coverage (Meyer et al. 2012;Prüfer et al. 2014) has spawned new methods to investigate the genetic basis of modern human traits that are not shared by the archaics (Pääbo 2014). One method, called 3P-CLR, models allele ...

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“…These rules use linguistic variables to assign statements using antecedents and consequents (IF-THEN). I delimited antecedent-consequent relationships based on a reading of Lahr's trait descriptions (1996), published accounts (Ahern 2006;Manzi et al 2000;Weaver 2009), and personal observation as to what was considered a Neandertal or modern feature. Fuzzy inference rules can use these rules in aggregate to calculate membership into "Neandertal" and "Modern" sets.…”

Section: The Fuzzy Inference Systemmentioning

confidence: 99%

“…Using breakpoints, variable states were collapsed into two states, usually describable as absence/presence or small/large (Table 3 and Figure 1). Breakpoints were identified through personal observation and published reports on Neandertal and modern human nonmetric characteristics (Ahern 2006;Manzi et al 2000;Weaver 2009). Each variable was treated as crisply determining group membership.…”

Section: Analysis 1: Both Variables and Group Membership Are Crispmentioning

confidence: 99%

Untitled

2012

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Recognizing fossil species, and reconstructing their phylogenetic relationships, is dependent in part on our ability to accurately record and analyze continuously distributed data. We usually classify specimens into groups (whether species or populations) by using crisp set theory. Fuzzy set theory can aid analysis in situations where populations have indistinct boundaries. Two primary areas of cladistic research contain elements of fuzzinessthe species concept itself, and the variables we use to analyze phylogenetic relationships among species. Analytical determination of species boundaries can be difficult due to hybridization as well as intra-and inter-specific variability. However, cladistic analysis requires that taxa are monophyletic, and unique in their morphological patterns. Variables used in cladistic analysis must be coded using discrete character states to determine polarity. But many morphological and metric variables are continuous or quasicontinuous in distribution, and are problematic for use in cladistic analyses without some type of non-overlapping dichotomization or breakpoint. The issue of how to utilize these continuously or quasicontinuously distributed variables, whether metric or nonmetric, is an ongoing issue in phylogenetic analysis. Fuzzy set theory is a method that circumvents two problematic assumptions implicit in phylogenetic analyses-crispness of taxa and crispness of traits. Using a fuzzy analysis, multiple character states are maintained through fuzzy variable sets that maintain the fuzziness of boundaries. Additionally, fuzzy analysis calculates a measure of the degree of group membership.To illustrate this process, I analyzed nine multistate nonmetric cranial variables representing three regions of the skull on 14 Neandertals and 24 early moderns using a Mamdani Fuzzy Inference System to compare the relative performance of fuzzy and crisp variables and groups on group identification. The analysis that performed best contained both fuzzy trait groups and fuzzy taxon groups. Fuzzy analysis is useful to explore the degree to which fuzziness is present in trait variation and in taxa, and it can advance our understanding of species identification and phylogeny construction. Expanding our toolkit to include fuzzy set analysis can help us determine how crisp or fuzzy are our putative taxonomic groups. "[T]he cult of impressive technicalities or the cult of precision may get the better of us, and interfere with our search for clarity, simplicity, and truth" (Popper 1983: 60). "The closer one looks at a real-world problem, the fuzzier becomes its solution" (Zadeh 1973: 28). INTRODUCTIONT here are many areas in paleoanthropology where precision eludes us. It is uncertain how many fossil species existed in the past; fossil sample sizes are small, and the magnitude and pattern of character variation within fossil species is unknown. It is unclear to what degree many characters are correlated, or are selectively neutral. Nonmetric characters may present as a continuous distributio...

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The meaning of Neandertal skeletal morphology

Cited by 125 publications

References 73 publications

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

Detecting ancient positive selection in humans using extended lineage sorting

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