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Baking with steel : the revolutionary new approach to perfect pizza, bread, and more
Shares cooking techniques and recipes from the creator of the Baking Steel, from breads and pizzas to cookies and ice cream-- Source other than Library of Congress.
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MHC class I diversity in chimpanzees and bonobos
Major histocompatibility complex (MHC) class I genes are critically involved in the defense against intracellular pathogens. MHC diversity comparisons among samples of closely related taxa may reveal traces of past or ongoing selective processes. The bonobo and chimpanzee are the closest living evolutionary relatives of humans and last shared a common ancestor some 1 mya. However, little is known concerning MHC class I diversity in bonobos or in central chimpanzees, the most numerous and genetically diverse chimpanzee subspecies. Here, we used a long-read sequencing technology (PacBio) to sequence the classical MHC class I genes
A
,
B
,
C
, and
A-like
in 20 and 30 wild-born bonobos and chimpanzees, respectively, with a main focus on central chimpanzees to assess and compare diversity in those two species. We describe in total 21 and 42 novel coding region sequences for the two species, respectively. In addition, we found evidence for a reduced MHC class I diversity in bonobos as compared to central chimpanzees as well as to western chimpanzees and humans. The reduced bonobo MHC class I diversity may be the result of a selective process in their evolutionary past since their split from chimpanzees.
Journal Article
The complete sequence and comparative analysis of ape sex chromosomes
Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility
1
. The X chromosome is vital for reproduction and cognition
2
. Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (
Pan paniscus
), chimpanzee (
Pan troglodytes
), western lowland gorilla (
Gorilla gorilla gorilla
), Bornean orangutan (
Pongo pygmaeus
) and Sumatran orangutan (
Pongo abelii
)) and a lesser ape (the siamang gibbon (
Symphalangus syndactylus
)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements—owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species.
Reference assemblies of great ape sex chromosomes show that Y chromosomes are more variable in size and sequence than X chromosomes and provide a resource for studies on human evolution and conservation genetics of non-human apes.
Journal Article
Great ape genetic diversity and population history
High-coverage sequencing of 79 (wild and captive) individuals representing all six non-human great ape species has identified over 88 million single nucleotide polymorphisms providing insight into ape genetic variation and evolutionary history and enabling comparison with human genetic diversity.
Genetic picture of endangered great apes
In an effort to provide insights into great ape genetic variation, the authors sequence 79 wild- and captive-born individuals from across all six great ape species and seven subspecies. Their data and analyses shed light on population structure and gene flow, inbreeding, inferred dynamics of effective population sizes and the differences in the rate of gene loss among the great apes. This new catalogue of great ape genome diversity provides a valuable resource for evolutionary and conservation studies.
Most great ape genetic variation remains uncharacterized
1
,
2
; however, its study is critical for understanding population history
3
,
4
,
5
,
6
, recombination
7
, selection
8
and susceptibility to disease
9
,
10
. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria–Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.
Journal Article
Characterization of Pan social systems reveals in-group/out-group distinction and out-group tolerance in bonobos
Human between-group interactions are highly variable, ranging from violent to tolerant and affiliative. Tolerance between groups is linked to our unique capacity for large-scale cooperation and cumulative culture, but its evolutionary origins are understudied. In chimpanzees, one of our closest living relatives, predominantly hostile between-group interactions impede cooperation and information flow across groups. In contrast, in our other closest living relative, the bonobo, tolerant between-group associations are observed. However, as these associations can be frequent and prolonged and involve social interactions that mirror those within groups, it is unclear whether these bonobos really do belong to separate groups. Alternatively, the bonobo grouping patterns may be homologous to observations from the large Ngogo chimpanzee community, where individuals form within-group neighborhoods despite sharing the same membership in the larger group. To characterize bonobo grouping patterns, we compare the social structure of the Kokolopori bonobos with the chimpanzee group of Ngogo. Using cluster analysis, we find temporally stable clusters only in bonobos. Despite the large spatial overlap and frequent interactions between the bonobo clusters, we identified significant association preference within but not between clusters and a unique space use of each cluster. Although bonobo associations are flexible (i.e., fission–fusion dynamics), cluster membership predicted the bonobo fission compositions and the spatial cohesion of individuals during encounters. These findings suggest the presence of a social system that combines clear in-group/out-group distinction and out-group tolerance in bonobos, offering a unique referential model for the evolution of tolerant between-group interactions in humans.
Journal Article
Lethal aggression in Pan is better explained by adaptive strategies than human impacts
A meta-analysis of studies on chimpanzees and bonobos across Africa shows that their conspecific aggression is the normal and expected product of adaptive strategies to obtain resources or mates and has no connection with the impacts of human activities.
Chimpanzees born to get wild
Studies of our closest living relatives, chimpanzees and bonobos, have been influential in efforts to understand the evolution of aggressive behaviour in our own species. In recent years, however, the validity of these studies has been questioned by proponents of the human impacts hypothesis, which argues that the occurrence of violence in chimpanzees is mainly the result of human activities. Now a meta-analysis of studies on chimpanzees and bonobos across Africa reveals that aggression between chimpanzees is the normal and expected product of adaptive strategies to obtain resources or mates, and has no connection with the presence or otherwise of human beings.
Observations of chimpanzees (
Pan troglodytes
) and bonobos (
Pan paniscus
) provide valuable comparative data for understanding the significance of conspecific killing. Two kinds of hypothesis have been proposed. Lethal violence is sometimes concluded to be the result of adaptive strategies, such that killers ultimately gain fitness benefits by increasing their access to resources such as food or mates
1
,
2
,
3
,
4
,
5
. Alternatively, it could be a non-adaptive result of human impacts, such as habitat change or food provisioning
6
,
7
,
8
,
9
. To discriminate between these hypotheses we compiled information from 18 chimpanzee communities and 4 bonobo communities studied over five decades. Our data include 152 killings (
n
= 58 observed, 41 inferred, and 53 suspected killings) by chimpanzees in 15 communities and one suspected killing by bonobos. We found that males were the most frequent attackers (92% of participants) and victims (73%); most killings (66%) involved intercommunity attacks; and attackers greatly outnumbered their victims (median 8:1 ratio). Variation in killing rates was unrelated to measures of human impacts. Our results are compatible with previously proposed adaptive explanations for killing by chimpanzees, whereas the human impact hypothesis is not supported.
Journal Article
Metabolic acceleration and the evolution of human brain size and life history
Compared to other apes, humans live longer, reproduce faster and have larger brains; here, total energy expenditure is studied in humans and all species of great ape, and is shown to be significantly higher in humans, demonstrating that the human lineage has experienced an energy-boosting acceleration in metabolic rate.
Metabolic factors in human evolution
Humans live longer than other apes, reproduce faster and have larger brains. This uniquely human portfolio of metabolically costly traits suggests that at some point in the hominin lineage there was a relaxation of energetic constraints, but the underlying mechanisms involved remain largely unknown. Here Herman Pontzer
et al
. study total energy expenditure in humans and all known species of great ape. They also revisit the archival data that seemed to have confused the issue somewhat. The authors conclude that total energy expenditure is significantly higher in humans, and that this is related to fat mass and particularly to brain mass. Thus human evolution owes much to an increased metabolic rate, along with changes in energy allocation, one result being our predisposition to deposit fat, whilst other hominoids remain relatively lean.
Humans are distinguished from the other living apes in having larger brains and an unusual life history that combines high reproductive output with slow childhood growth and exceptional longevity
1
. This suite of derived traits suggests major changes in energy expenditure and allocation in the human lineage, but direct measures of human and ape metabolism are needed to compare evolved energy strategies among hominoids. Here we used doubly labelled water measurements of total energy expenditure (TEE; kcal day
−1
) in humans, chimpanzees, bonobos, gorillas and orangutans to test the hypothesis that the human lineage has experienced an acceleration in metabolic rate, providing energy for larger brains and faster reproduction without sacrificing maintenance and longevity. In multivariate regressions including body size and physical activity, human TEE exceeded that of chimpanzees and bonobos, gorillas and orangutans by approximately 400, 635 and 820 kcal day
−1
, respectively, readily accommodating the cost of humans’ greater brain size and reproductive output. Much of the increase in TEE is attributable to humans’ greater basal metabolic rate (kcal day
−1
), indicating increased organ metabolic activity. Humans also had the greatest body fat percentage. An increased metabolic rate, along with changes in energy allocation, was crucial in the evolution of human brain size and life history.
Journal Article
Comparative analysis of intragroup intermale relationships: a study of wild bonobos (Pan paniscus) in Wamba, Democratic Republic of Congo and chimpanzees (Pan troglodytes) in Kalinzu Forest Reserve, Uganda
Although chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) share a multi-male/multi-female societal organization and form male-philopatric groups, disparities in terms of male aggression and stability of temporary parties are thought to exist among them. However, existing research in bonobos has mainly focused on the high social status, prolonged receptivity, and characteristic sexual behaviors of females, leaving the behaviors of males understudied. Moreover, prior comparative studies on Pan suffer from methodological inconsistencies. This study addresses these gaps by employing a uniform observation method to explore party attendance and aggressive interactions among male bonobos in Wamba and male chimpanzees in Kalinzu. Unlike male chimpanzees, which exhibit dispersion in the absence of receptive females in the group, male bonobos showed a lesser degree of such dispersion. Although the overall frequency of aggressive interactions per observation unit did not significantly differ between the two species, the nature of these interactions varied. Notably, severe aggressive behaviors such as physical confrontations among adult males were absent in bonobos, with most aggression occurring between the sons of the two highest-ranking females. Additionally, in bonobos, females actively engaged in polyadic aggressive behavior as aggressors, while all instances of coalitionary aggression in chimpanzees originated from male aggressors. These findings underscore the substantial impact of female behaviors on the observed distinctions in male aggressive interactions between the two species.
Journal Article
The bonobo genome compared with the chimpanzee and human genomes
Sequencing of the bonobo genome shows that more than three per cent of the human genome is more closely related to either the bonobo genome or the chimpanzee genome than those genomes are to each other.
Bonobo genome completes ape set
The chimpanzee and the bonobo are our species' two closest living relatives. This paper reports the genome sequence of the bonobo, the last ape to be sequenced. Comparative genomic analyses reveal that more than 3% of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. The results shed light on the ancestry of the two ape species and might eventually help us to understand the genetic basis of phenotypes that humans share with one or the other ape species.
Two African apes are the closest living relatives of humans: the chimpanzee (
Pan troglodytes
) and the bonobo (
Pan paniscus
). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours
1
,
2
,
3
,
4
, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.
Journal Article