scholarly journals Divergence, demography and gene loss along the human lineage

2010 ◽  
Vol 365 (1552) ◽  
pp. 2451-2457 ◽  
Author(s):  
Hie Lim Kim ◽  
Takeshi Igawa ◽  
Ayaka Kawashima ◽  
Yoko Satta ◽  
Naoyuki Takahata
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Homo Sapiens ◽  
Divergence Time ◽  
Cell Receptor ◽  
Middle Pleistocene ◽  
Human Lineage ◽  
Modern Humans ◽  
Olfactory Receptor Genes ◽  
Living Organisms

Genomic DNA sequences are an irreplaceable source for reconstructing the vanished past of living organisms. Based on updated sequence data, this paper summarizes our studies on species divergence time, ancient population size and functional loss of genes in the primate lineage leading to modern humans ( Homo sapiens sapiens ). The inter- and intraspecific comparisons of DNA sequences suggest that the human lineage experienced a rather severe bottleneck in the Middle Pleistocene, throughout which period the subdivided African population played a predominant role in shaping the genetic architecture of modern humans. Also, published and newly identified human-specific pseudogenes (HSPs) are enumerated in order to infer their significance for human evolution. Of the 121 candidate genes obtained, authentic HSPs turn out to comprise only 25 olfactory receptor genes, four T cell receptor genes and nine other genes. The fixation of HSPs has been too rare over the past 6–7 Myr to account for species differences between humans and chimpanzees.

scholarly journals Dental evolutionary rates and its implications for the Neanderthal–modern human divergence

2019 ◽  
Vol 5 (5) ◽  
pp. eaaw1268 ◽  
Author(s):  
Aida Gómez-Robles
Keyword(s):  
Divergence Time ◽  
Modern Human ◽  
Evolutionary Rates ◽  
Middle Pleistocene ◽  
Last Common Ancestor ◽  
Modern Humans ◽  
Bayesian Analyses ◽  
Sima De Los Huesos ◽  
Dental Evolution ◽  
Quantitative Analyses

The origin of Neanderthal and modern human lineages is a matter of intense debate. DNA analyses have generally indicated that both lineages diverged during the middle period of the Middle Pleistocene, an inferred time that has strongly influenced interpretations of the hominin fossil record. This divergence time, however, is not compatible with the anatomical and genetic Neanderthal affinities observed in Middle Pleistocene hominins from Sima de los Huesos (Spain), which are dated to 430 thousand years (ka) ago. Drawing on quantitative analyses of dental evolutionary rates and Bayesian analyses of hominin phylogenetic relationships, I show that any divergence time between Neanderthals and modern humans younger than 800 ka ago would have entailed unexpectedly rapid dental evolution in early Neanderthals from Sima de los Huesos. These results support a pre–800 ka last common ancestor for Neanderthals and modern humans unless hitherto unexplained mechanisms sped up dental evolution in early Neanderthals.

scholarly journals On the estimation of ancestral population sizes of modern humans

1997 ◽  
Vol 69 (2) ◽  
pp. 111-116 ◽  
Author(s):  
ZIHENG YANG
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Divergence Time ◽  
Ancestral Population ◽  
Rate Variation ◽  
Effective Population ◽  
Modern Humans ◽  
Extant Species ◽  
Population Sizes ◽  
Highly Correlated

The theory developed by Takahata and colleagues for estimating the effective population size of ancestral species using homologous sequences from closely related extant species was extended to take account of variation of evolutionary rates among loci. Nuclear sequence data related to the evolution of modern humans were reanalysed and computer simulations were performed to examine the effect of rate variation on estimation of ancestral population sizes. It is found that the among-locus rate variation does not have a significant effect on estimation of the current population size when sequences from multiple loci are sampled from the same species, but does have a significant effect on estimation of the ancestral population size using sequences from different species. The effects of ancestral population size, species divergence time and among-locus rate variation are found to be highly correlated, and to achieve reliable estimates of the ancestral population size, effects of the other two factors should be estimated independently.

scholarly journals Anchored Hybrid Enrichment-Based Phylogenomics of Leafhoppers and Treehoppers (Hemiptera: Cicadomorpha: Membracoidea)

2017 ◽  
Vol 1 (1) ◽  
pp. 57-72 ◽  
Author(s):  
Christopher H Dietrich ◽  
Julie M Allen ◽  
Alan R Lemmon ◽  
Emily Moriarty Lemmon ◽  
Daniela M Takiya ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Single Gene ◽  
Gene Tree ◽  
Divergence Time ◽  
Data Set ◽  
Nucleotide Sequence Data ◽  
Divergence Time Estimates ◽  
Morphological Criteria ◽  
Anchored Hybrid Enrichment

Abstract A data set comprising DNA sequences from 388 loci and >99,000 aligned nucleotide positions, generated using anchored hybrid enrichment, was used to estimate relationships among 138 leafhoppers and treehoppers representative of all major lineages of Membracoidea, the most diverse superfamily of hemipteran insects. Phylogenetic analysis of the concatenated nucleotide sequence data set using maximum likelihood produced a tree with most branches receiving high support. A separate coalescent gene tree analysis of the same data generally recovered the same strongly supported clades but was less well resolved overall. Several nodes pertaining to relationships among leafhopper subfamilies currently recognized based on morphological criteria were separated by short internodes and received low support. Although various higher taxa were corroborated with improved branch support, relationships among some major lineages of Membracoidea are only somewhat more resolved than previously published phylogenies based on single gene regions or morphology. In agreement with previous studies, the present results indicate that leafhoppers (Cicadellidae) are paraphyletic with respect to the three recognized families of treehoppers (Aetalionidae, Melizoderidae, and Membracidae). Divergence time estimates indicate that most of the poorly resolved divergence events among major leafhopper lineages occurred during the lower to middle Cretaceous and that most modern leafhopper subfamilies, as well as the lineage comprising the three recognized families of treehoppers, also arose during the Cretaceous.

scholarly journals Scalable Classification of Organisms into a Taxonomy Using Hierarchical Supervised Learners

2020 ◽  
Author(s):  
Gihad N. Sohsah ◽  
Ali Reza Ibrahimzada ◽  
Huzeyfe Ayaz ◽  
Ali Cakmak
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Kernel Method ◽  
Sequence Data ◽  
Dna Barcode ◽  
Living Organism ◽  
Large Datasets ◽  
Living Organisms ◽  
Hierarchical Classifier

Taxonomy of living organisms gains major importance in making the study of vastly heterogeneous living things easier. In addition, various fields of applied biology (e.g., agriculture) depend on classification of living creatures. Specific fragments of the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are prealigned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification accuracy. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from BOLD systems. We demonstrate that the proposed framework provides higher accuracy than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high accuracy and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.

The Morphological and Behavioural Origins of Modern Humans

2004 ◽  
Author(s):  
Chris Stringer
Keyword(s):  
Homo Sapiens ◽  
Modern Human ◽  
Human Behaviour ◽  
Genetic Evidence ◽  
Middle Pleistocene ◽  
African Origin ◽  
Modern Humans ◽  
Speciation Event ◽  
Out Of Africa

This chapter provides an update on the speciation of modern Homo sapiens and the Out of Africa hypothesis. The majority of the fossil and genetic evidence favours an African origin for modern humans during the later part of the Middle Pleistocene (prior to 130,000 years ago), and one or more range expansions out of Africa after that date. However, a number of uncertainties remain. If there was a speciation event at the appearance of modern humans, what was its nature? Furthermore, did the evolution of modern human behaviour occur gradually or punctuationally? The discussion examines the difficulties faced in defining what is meant by ‘modern’ humans, and in reconstructing the morphological and behavioural origins of our species.

scholarly journals Systematic Approach to Establish DNA Barcode of Medicinally Important Plants in Nepal

2019 ◽  
Vol 8 ◽  
pp. 57-61
Author(s):  
Sunil Bhandari ◽  
Jay Bhandari ◽  
Sanjay Lama
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Dna Barcode ◽  
Sequence Information ◽  
Terrestrial Plants ◽  
Coding Region ◽  
Global Database ◽  
High Efficient ◽  
Living Organisms

DNA barcoding is an emerging tool for species identification that uses internationally agreed protocols and regions of DNA to create a global database of living organisms. Initiatives are taking place to generate DNA ba rcodes for all groups of living organisms make these genomic identity publically available to understand, conserve, and utilize the world 's biodiversity. Most of the terrestrial plants are characterized using two section of coding region within chloplast, part of chloroplast gene, a more conserved rbcl and more polymorphic MatK gene. In order to create high quality databases, each plants are characterized not only with the rbcl and MatK DNA sequences, an additional sequence information from internal transcribed spacer (ITS) region is more efficient. The quality of barcode depends on the various factors such as efficient primers, purity of DNA templates, as well as the quality of PCR amplicon from which the sequence data will derive. The protocol described here led to the generation of high efficient PCR amplicon which will aid in the minimization of erroneous DNA sequence infonnation from which bioinformatics procedure will generate efficient barcodes. The primers used to amplified MatK, rbcl and ITS sequence were MatK-4 13f-1 and MatK- 1227r-1, rbcl-1F and rbcl-724R, ITS1 and ITS4 showed a strong amplification successes of 80% of each in the tasted medicinal plants of Nepal. This study propose that the used sets of primers and amplification condition will help, in part, the development of DNA barcode for medicinally important plants of Nepal to conserve their identity with its nativeness.

scholarly journals Estimating divergence times from DNA sequences

Genetics ◽  
2021 ◽  
Author(s):  
Per Sjödin ◽  
James McKenna ◽  
Mattias Jakobsson
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Divergence Time ◽  
Ancestral Population ◽  
Population Divergence ◽  
Model Parameters ◽  
Human Populations ◽  
Computationally Efficient ◽  
Evolutionary Forces ◽  
Diploid Individual

Abstract The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the ‘Two-Two (TT)’ and the ‘Two-Two-outgroup (TTo)’ methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split-times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo-method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.

scholarly journals Estimating divergence times from DNA sequences

2020 ◽  
Author(s):  
Per Sjödin ◽  
James McKenna ◽  
Mattias Jakobsson
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Divergence Time ◽  
Ancestral Population ◽  
Population Divergence ◽  
Model Parameters ◽  
Human Populations ◽  
Computationally Efficient ◽  
Evolutionary Forces ◽  
Diploid Individual

ABSTRACTThe patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the ‘Two-Two (TT)’ and the ‘Two-Two-outgroup (TTo)’ methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split-times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo-method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.

Neanderthals and modern humans

2017 ◽  
Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde
Keyword(s):  
Genetic Differentiation ◽  
Nuclear Dna ◽  
Homo Sapiens ◽  
Whole Genome ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Homo Neanderthalensis ◽  
Modern Mind ◽  
Similarities And Differences ◽  
Mode 3

This chapter deals with the similarities and differences between Homo neanderthalensis and Homo sapiens, by considering genetic, brain, and cognitive evidence. The genetic differentiation emerges from fossil genetic evidence obtained first from mtDNA and later from nuclear DNA. With high throughput whole genome sequencing, sequences have been obtained from the Denisova Cave (Siberia) fossils. Nuclear DNA of a third species (“Denisovans”) has been obtained from the same cave and used to define the phylogenetic relationships among the three species during the Upper Palaeolithic. Archaeological comparisons make it possible to advance a four-mode model of the evolution of symbolism. Neanderthals and modern humans would share a “modern mind” as defined up to Symbolic Mode 3. Whether the Neanderthals reached symbolic Mode 4 remains unsettled.

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