A Pleistocene population X-plosion?
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Animals↗
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Rates of divergence in gene expression profiles of primates, mice, and flies: stabilizing selection and variability among functional categories.
The extent to which natural selection shapes phenotypic variation has long been a matter of debate among those studying organic evolution. We studied the patterns of gene expression polymorphism and divergence in several datasets that ranged from comparisons between two very closely related laboratory strains of mice to comparisons across a considerably longer time scale, such as between humans and chimpanzees, two species of mice, and two species of Drosophila. The results were analyzed and interpreted in view of neutral models of phenotypic evolution. Our analyses used a number of metrics to show that most mRNA levels are evolutionary stable, changing little across the range of taxonomic distances compared. This implies that, overall, widespread stabilizing selection on transcription levels has prevented greater evolutionary changes in mRNA levels. Nevertheless, the range of rates of divergence is large with highly significant differences in the rate and patterns of transcription divergence across functional classes defined on the basis of the gene ontology annotation (primates and mice datasets) or on the basis of the pattern of sex-biased gene expression (Drosophila). Moreover, rates of divergence of sex-biased genes in the contrast between Drosophila species show a distinct pattern from that observed in the contrast between populations of D. melanogaster. Hence, we discuss the time scale of the changes observed and its consequences for the relationship between variation in gene expression within and between species. Finally, we argue that differences in mRNA levels of the magnitudes observed herein could be explained by a remarkably small number of generations of directional selection.
Animals↗
Assessment the genetic diversity of Auricularia strains by two PCR-based typing methods.
Two PCR-based methods, enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) and randomly amplified polymorphic DNA (RAPD), were adopted for differentiating Auricularia strains. Taken the similarity coefficient as 75%, 29 strains of three Auricularia species were grouped into 6 and 9 clusters by RAPD and ERIC, respectively. The dendrogram from ERIC exhibited two distinct parts, one representing A. auricula and the other A. polytricha, but the dendrogram from RAPD failed to clearly distinguish between these two species. However, both methods similarly revealed high homology between A. fuscosuccinea and A. auricula. The homology relationships among the three species obtained from ERIC were validated by Southern hybridization. The analyses showed that RAPD is able to differentiate mainly at the species level, while ERIC is effective at the strain level and therefore more consistent with cultivation characteristics. The results indicate that the method of ERIC-PCR is more rapid and reliable than RAPD, and may substitute for RAPD in research related to the genetic identification and genetic diversity in Auricularia.
Agaricales↗
Pan-analysis of intra- and inter-species diversity reveals a group of highly variable immune receptor genes in rice.
Plant immune receptors and their natural variations play a central role in combating disease-causing pathogens. These immune receptors include intracellular nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) and cell-surface pattern recognition receptors (PRRs) that can be further classified as receptor-like proteins (RLPs) and receptor-like kinases (RLKs). Although the NLRome has been characterized, the repertoire and extent of diversity of PRRome remain undetermined in rice. In this study, we examined the diversity of immune receptor genes using high-quality genomes of 309 rice accessions from 8 species within the genus Oryza. A total of 376 310 immune receptor genes were identified, including 149 592 NLR-coding genes and 226 718 PRR coding genes. Shannon entropy analysis revealed a set of immune receptors that display significant intra-species and inter-species diversity in rice. In general, RLPs are more variable than RLKs, while NLRs and LRR-RLPs are more variable than LRR-RLKs. Additionally, NLR and PRR genes exhibit contrasting shoot/root expression patterns, with NLRs generally skewed towards root expression. Furthermore, we found that the size of the LRR-RLK gene families correlates with local annual precipitation, suggesting a stronger selection pressure on LRR-RLK genes in rice accessions grown under wet conditions than dry conditions. In sum, this pan-genomic analysis not only reveals the extensive diversity of the immune receptor repertoires in rice but also provides potential target genes for improving disease resistance in rice.
Oryza↗
Genomic insights into karyotype evolution and adaptive mechanisms in Polygonaceae species.
Polygonaceae, with ecological versatility and global distribution, is an ideal system for investigating plant adaptation. However, the genomic mechanisms underlying its karyotype evolution and environmental resilience remain unclear. We herein present chromosome-level genomes of 11 species from 10 Polygonaceae genera. Our analyses reveal that Gypsy retrotransposons are key drivers of genome size variations in Polygonaceae. We reconstructed a Polygonaceae ancestral karyotype comprising 28 proto-chromosomes and elucidated evolutionary trajectories via extensive chromosomal rearrangements. Furthermore, we constructed a cross-genus super pan-genome for Polygonaceae, identifying 80,055 gene families, of which 9,845 (12.30%) are core gene families. Private genes are found to contribute significantly to interspecific differences in adaptability. Notably, gene copy number variations are identified as a critical factor influencing adaptations to diverse niches involving species-specific increases in metabolic pathways. This study provides a genomic framework for Polygonaceae karyotype plasticity and adaptive innovation, offering insights into plant evolution under environmental challenges.
Karyotype↗
Hotspots for copy number variation in chimpanzees and humans.
Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number variation in nonhuman primates. We have used two array-based comparative genomic hybridization platforms to identify a total of 355 copy number variants (CNVs) in the genomes of 20 wild-born chimpanzees (Pan troglodytes) and have compared the identified chimpanzee CNVs to known human CNVs from previous studies. Many CNVs were observed in the corresponding regions in both chimpanzees and humans; especially those CNVs of higher frequency. Strikingly, these loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formation through nonallelic homologous recombination mechanisms. Therefore, some of these regions may be unstable "hotspots" for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species.
Animals↗
Quantifying temporal bone morphology of great apes and humans: an approach using geometric morphometrics.
The hominid temporal bone offers a complex array of morphology that is linked to several different functional systems. Its frequent preservation in the fossil record gives the temporal bone added significance in the study of human evolution, but its morphology has proven difficult to quantify. In this study we use techniques of 3D geometric morphometrics to quantify differences among humans and great apes and discuss the results in a phylogenetic context. Twenty-three landmarks on the ectocranial surface of the temporal bone provide a high level of anatomical detail. Generalized Procrustes analysis (GPA) is used to register (adjust for position, orientation and scale) landmark data from 405 adults representing Homo, Pan, Gorilla and Pongo. Principal components analysis of residuals from the GPA shows that the major source of variation is between humans and apes. Human characteristics such as a coronally orientated petrous axis, a deep mandibular fossa, a projecting mastoid process, and reduced lateral extension of the tympanic element strongly impact the analysis. In phenetic cluster analyses, gorillas and orangutans group together with respect to chimpanzees, and all apes group together with respect to humans. Thus, the analysis contradicts depictions of African apes as a single morphotype. Gorillas and orangutans lack the extensive preglenoid surface of chimpanzees, and their mastoid processes are less medially inflected. These and other characters shared by gorillas and orangutans are probably primitive for the African hominid clade.
Adult↗
Genetic influence on the expression of hand preferences in chimpanzees (Pan troglodytes): evidence in support of the right-shift theory and developmental instability.
Genetic mechanisms have been proposed to explain the pervasive representation of right-handedness in humans, whereas random, nongenetic factors have been posited to explain the lack of population-level right-handedness in nonhuman primates. We report evidence that hand preferences in chimpanzees are heritable, even among related individuals raised in different environments. Furthermore, we report that the degree of heritability is modified by factors associated with developmental instability, notably, offspring parity. The data are interpreted to reconcile both genetic models for handedness and hypotheses suggesting that developmental instability influences variation in handedness.
Animals↗
Individual and evolutionary variation of primate ribosomal DNA transcription initiation regions.
A 16-kilobase region surrounding the transcription initiation site for ribosomal DNA and including the entire ribosomal DNA transcription unit has been characterized in man and compared in higher primates. Restriction analysis of ribosomal DNA from the pygmy chimpanzee (Pan paniscus), the common chimpanzee (Pan troglodytes), the gorilla (Gorilla gorilla), the orangutan (Pongo pygmaeus), the gibbon (Hylobates lar), and the rhesus monkey (Macaca mulatta) allows a primate phylogeny to be constructed based on ribosomal DNA structure. Individual variation and methylation are demonstrated in the ribosomal DNA repeats of all primates examined. Restriction analysis with HincII endonuclease suggests cleavage at sites containing methylated CpG and adds the SalI/HincII pair to those enzymes useful for studying DNA modification.
Animals↗
Construction of a cucumber genetic linkage map with SRAP markers and location of the genes for lateral branch traits.
Using SRAP (sequence-related amplified polymorphism) markers a genetic linkage map of cucumber was constructed with a population consisting of 138 F2 individuals derived from a cross of the two cucumber lines, S06 and S52. In the survey of parental polymorphisms with 182 primer combinations, 64 polymorphism-revealing primer pairs were screened out, which generated totally 108 polymorphic bands with an average of 1.7 bands per primer pair and at most 6 bands from one primer pair. The constructed molecular linkage map included 92 loci, distributed in seven linkage groups and spanning 1164.2 cM in length with an average genetic distance of 12.6 cM between two neighboring loci. Based on this linkage map, the quantitative trait loci (QTL) for the lateral branch number (Ibn) and the lateral branch average length (Ibl) in cucumber were identified by QTLMapperl.6. A major QTL Ibn1 located between ME11 SA4B and ME5EM5 in LG2 could explain 10.63% of the total variation with its positively effecting allele from S06. A major QTL Ibl1 located between DC1OD3 and DC1EM14 in LG2 could account for 10.38% of the total variation with its positively effecting allele from S06.
Chromosome Mapping↗
Muscle architecture of the common chimpanzee (Pan troglodytes): perspectives for investigating chimpanzee behavior.
Thorpe et al. (Am J Phys Anthropol 110:179-199, 1999) quantified chimpanzee (Pan troglodytes) muscle architecture and joint moment arms to determine whether they functionally compensated for structural differences between chimpanzees and humans. They observed enough distinction to conclude that musculoskeletal properties were not compensatory and suggested that chimpanzees and humans do not exhibit dynamically similar movements. These investigators based their assessment on unilateral limb musculatures from three male chimpanzees, of which they called one non-adult representative. Factors such as age, sex, and behavioral lateralization may be responsible for variation in chimpanzee muscle architecture, but this is presently unknown. While the full extent of variation in chimpanzee muscle architecture due to such factors cannot be evaluated with data presently available, the present study expands the chimpanzee dataset and provides a preliminary glimpse of the potential relevance of these factors. Thirty-seven forelimb and 36 hind limb muscles were assessed in two chimpanzee cadavers: one unilaterally (right limbs), and one bilaterally. Mass, fiber length, and physiological cross-sectional area (PCSA) are reported for individual muscles and muscle groups. The musculature of an adult female is more similar in architectural patterns to a young male chimpanzee than to humans, particularly when comparing muscle groups. Age- and sex-related intraspecific differences do not obscure chimpanzee-human interspecific differences. Side asymmetry in one chimpanzee, despite consistent forelimb directional asymmetry, also does not exceed the magnitude of chimpanzee-human differences. Left forelimb muscles, on average, usually had higher masses and longer fiber lengths than right, while right forelimb muscles, on average, usually had greater PCSAs than left. Most muscle groups from the left forelimb exhibited greater masses than right groups, but group asymmetry was significant only for the manual digital muscles. The hind limb exhibited less asymmetry than the forelimb in most comparisons. Examination of additional chimpanzees would clarify the full range of inter- and intra-individual variation.
Animals↗
Further studies on quasi-continuous variations in Hominoidea.
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Animals↗
Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees.
To study the genomic divergences among hominoids and to estimate the effective population size of the common ancestor of humans and chimpanzees, we selected 53 autosomal intergenic nonrepetitive DNA segments from the human genome and sequenced them in a human, a chimpanzee, a gorilla, and an orangutan. The average sequence divergence was only 1.24% +/- 0.07% for the human-chimpanzee pair, 1.62% +/- 0.08% for the human-gorilla pair, and 1.63% +/- 0.08% for the chimpanzee-gorilla pair. These estimates, which were confirmed by additional data from GenBank, are substantially lower than previous ones, which included repetitive sequences and might have been based on less-accurate sequence data. The average sequence divergences between orangutans and humans, chimpanzees, and gorillas were 3.08% +/- 0.11%, 3.12% +/- 0.11%, and 3.09% +/- 0.11%, respectively, which also are substantially lower than previous estimates. The sequence divergences in other regions between hominoids were estimated from extensive data in GenBank and the literature, and Alus showed the highest divergence, followed in order by Y-linked noncoding regions, pseudogenes, autosomal intergenic regions, X-linked noncoding regions, synonymous sites, introns, and nonsynonymous sites. The neighbor-joining tree derived from the concatenated sequence of the 53 segments--24,234 bp in length--supports the Homo-Pan clade with a 100% bootstrap value. However, when each segment is analyzed separately, 22 of the 53 segments (approximately 42%) give a tree that is incongruent with the species tree, suggesting a large effective population size (N(e)) of the common ancestor of Homo and Pan. Indeed, a parsimony analysis of the 53 segments and 37 protein-coding genes leads to an estimate of N(e) = 52,000 to 96,000. As this estimate is 5 to 9 times larger than the long-term effective population size of humans (approximately 10,000) estimated from various genetic polymorphism data, the human lineage apparently had experienced a large reduction in effective population size after its separation from the chimpanzee lineage. Our analysis assumes a molecular clock, which is in fact supported by the sequence data used. Taking the orangutan speciation date as 12 to 16 million years ago, we obtain an estimate of 4.6 to 6.2 million years for the Homo-Pan divergence and an estimate of 6.2 to 8.4 million years for the gorilla speciation date, suggesting that the gorilla lineage branched off 1.6 to 2.2 million years earlier than did the human-chimpanzee divergence.
Alu Elements↗
Biometrical studies upon hominoid teeth: the coefficient of variation, sexual dimorphism and questions of phylogenetic relationship.
Sexual dimorphism as a function of variation in hominoid tooth metrics has been investigated for four groups of taxa: Recent great apes (two subfamilies), Dryopiths (one subfamily), Ramapiths (one subfamily) and hominids (one family). Gorilla, and to a lesser extent Pan, appear characterized by very high levels of sexual dimorphism and meet several criteria for statistical outliers. Recent great apes are the only group exhibiting consistently high levels of sexual dimorphism. Ramapiths are the only group characterized by low levels of sexual dimorphism and their relative canine length is most similar to Dryopiths. Both Dryopiths and hominids contain taxa with low and intermediate levels of sexual dimorphism. The Gingerich and Shoeninger hypothesis relating coefficients of variation to occlusal complexity is supported. Non-parametric statistics suggest that homogeneity of coefficient of variation profiles over most of the tooth row is characteristic of only the Dryopiths and a composite data set composed of the Dryopith plus Ramapith tooth measurements. Oxnard's model for the multifactorial basis of multiple sexual dimorphisms is also supported. The Dryopith and hominid patterns of sexual dimorphism are similar, an observation that suggests phylogenetic relationship. At the taxonomic level of subfamily or family, sexual dimorphism is a character of cladistic usefulness and possible phylogenetic valence. Assuming that breeding system and sexual dimorphism are functional correlates as many workers suggest, then Ramapithecus sp. China, Sivapithecus indicus and possibly Australopithecus boisei are good candidates for having possessed monogamous breeding/social structures. All Dryopith taxa, S. sivalensis, Sivapithecus sp. China, A. afarensis, Homo habilis and H. erectus emerge as the best candidates for having possessed a polygynous breeding/social structure. No biometrical affinities of Ramapiths with hominids can be demonstrated and some phylogenetic relationship with Dryopiths is suggested. Kay's interpretation of Ramapith sexual dimorphism and taxonomic affinity is not supported. The lack of control over temporal and geographic range variation is discussed and the loose association of these variables with differences in tooth morphology is noted. The high heritability of tooth size also suggests that assignment of "high" or "low" index values to extinct taxa as a measure that describes evolving clades at discrete points in evolutionary time is appropriate.(ABSTRACT TRUNCATED AT 400 WORDS)
Animals↗
The origami of thioredoxin-like folds.
Origami is the Japanese art of folding a piece of paper into complex shapes and forms. Much like origami of paper, Nature has used conserved protein folds to engineer proteins for a particular task. An example of a protein family, which has been used by Nature numerous times, is the thioredoxin superfamily. Proteins in the thioredoxin superfamily are all structured with a beta-sheet core surrounded with alpha-helices, and most contain a canonical CXXC motif. The remarkable feature of these proteins is that the link between them is the fold; however, their reactivity is different for each member due to small variations in this general fold as well as their active site. This review attempts to unravel the minute differences within this protein family, and it also demonstrates the ingenuity of Nature to use a conserved fold to generate a diverse collection of proteins to perform a number of different biochemical tasks.
Amino Acid Motifs↗
Early hominin limb proportions.
Recent analyses and new fossil discoveries suggest that the evolution of hominin limb length proportions is complex, with evolutionary reversals and a decoupling of proportions within and between limbs. This study takes into account intraspecific variation to test whether or not the limb proportions of four early hominin associated skeletons (AL 288-1, OH 62, BOU-VP-12/1, and KNM-WT 15000) can be considered to be significantly different from one another. Exact randomization methods were used to compare the differences between pairs of fossil skeletons to the differences observed between all possible pairs of individuals within large samples of Gorilla gorilla, Pan troglodytes, Pongo pygmaeus, and Homo sapiens. Although the difference in humerofemoral proportions between OH 62 and AL 288-1 does not exceed variation in the extant samples, it is rare. When humerofemoral midshaft circumferences are compared, the difference between OH 62 and AL 288-1 is fairly common in extant species. This, in combination with error associated with the limb lengths estimates, suggests that it may be premature to consider H. (or Australopithecus) habilis as having more apelike limb proportions than those in A. afarensis. The humerofemoral index of BOU-VP-12/1 differs significantly from both OH 62 and AL 288-1, but not from KNM-WT 15000. Published length estimates, if correct, suggest that the relative forearm length of BOU-VP-12/1 is unique among hominins, exceeding those of the African apes and resembling the proportions in Pongo. Evidence that A. afarensis exhibited a less apelike upper:lower limb design than A. africanus (and possibly H. habilis) suggests that, if A. afarensis is broadly ancestral to A. africanus, the latter did not simply inherit primitive morphology associated with arboreality, but is derived in this regard. The fact that the limb proportions of OH 62 (and possibly KNM-ER 3735) are no more human like than those of AL 288-1 underscores the primitive body design of H. habilis.
Animals↗
Amplification of a complete simian immunodeficiency virus genome from fecal RNA of a wild chimpanzee.
Current knowledge of the genetic diversity of simian immunodeficiency virus (SIVcpz) infection of wild chimpanzees (Pan troglodytes) is incomplete since few isolates, mostly from captive apes from Cameroon and Gabon, have been characterized; yet this information is critical for understanding the origins of human immunodeficiency virus type 1 (HIV-1) and the circumstances leading to the HIV-1 pandemic. Here, we report the first full-length SIVcpz sequence (TAN1) from a wild chimpanzee (Pan troglodytes schweinfurthii) from Gombe National Park (Tanzania), which was obtained noninvasively by amplification of virion RNA from fecal samples collected under field conditions. Using reverse transcription-PCR and a combination of generic and strain-specific primers, we amplified 13 subgenomic fragments which together spanned the entire TAN1 genome (9,326 bp). Distance and phylogenetic tree analyses identified TAN1 unambiguously as a member of the HIV-1/SIVcpz group of viruses but also revealed an extraordinary degree of divergence from all previously characterized SIVcpz and HIV-1 strains. In Gag, Pol, and Env proteins, TAN1 differed from west-central African SIVcpz and HIV-1 strains on average by 36, 30, and 51% of amino acid sequences, respectively, approaching distance values typically found for SIVs from different primate species. The closest relative was SIVcpzANT, also from a P. t. schweinfurthii ape, which differed by 30, 25, and 44%, respectively, in these same protein sequences but clustered with TAN1 in all major coding regions in a statistically highly significant manner. These data indicate that east African chimpanzees, like those from west-central Africa, are naturally infected by SIVcpz but that their viruses comprise a second, divergent SIVcpz lineage which appears to have evolved in relative isolation for an extended period of time. Our data also demonstrate that noninvasive molecular epidemiological studies of SIVcpz in wild chimpanzees are feasible and that such an approach may prove essential for unraveling the evolutionary history of SIVcpz/HIV-1 as well as that of other pathogens naturally infecting wild primate populations.
Amino Acid Sequence↗
Chimpanzees as an outgroup for the examination of human dental evolution.
In the assessment of human origins, chimpanzees (Pan troglodytes, henceforth called Pan) represent the best hominoid outgroup for comparisons. Such an outgroup roots the "anatomically modern" human population cluster, or continuum. This study incorporates chimpanzees into a worldwide modern human database of quantified complete tooth variables (approximately 30 per tooth; e.g., root, pulp, enamel) in an attempt to develop a more accurate phylogeny of the hominoid continuum, with only intervening extinct hominids missing. Canonical discriminate analysis was performed mainly among Liberian common chimpanzees and global samples of humans. The first canonical variable explained 70% of the total variance and showed a tight cluster of humans, with chimpanzees as a distant outgroup. Within the human community, first non-San Bushman, sub-Saharan Africans and Andamanese, and then, close in, Australian aborigines were positioned towards Pan. Their relative orientation suggested an African human origin with the first branch within sub-Saharan Africa: sub-Saharan Africans and San Bushmen. Next, Andamanese Negritos, and then Australian aborigines, formed the early first surviving modern human lineage to leave Africa. Thin enamel and big teeth with relatively large roots characterized Pan nonmolar teeth. Humans showed a generalized sexual dimorphism for all teeth, with males having bigger teeth, bigger relative roots, and thinner enamel than females, while only Pan canines had significant and impressive sexual dimorphism. Interestingly, Pan molars were not larger than human molars. The data suggest that although hominids underwent two dental macroevolutionary events, the lineage leading to modern humans only experienced anterior tooth-size reduction. The suggested evolutionary significance of the observed total tooth variation is discussed.
Analysis of Variance↗