Identifying conservation units within captive chimpanzee populations

Deinard, Amos S.; Kídd, Kenneth K.

doi:10.1002/(sici)1096-8644(200001)111:1<25::aid-ajpa3>3.0.co;2-r

Cited by 39 publications

(23 citation statements)

References 61 publications

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“…Our results, as well as analyses of single gene regions on mtDNA (3), the X chromosome (9), and the autosomes (8,19) all support greater diversity in Pan. These findings stand in direct contrast to the multilocus data of Wise et al (45), who claimed that human autosomal short tandem repeat heterozygosity was significantly greater than that of chimpanzees.…”

Section: Discussionsupporting

confidence: 64%

“…If we take the average level of human nucleotide heterozygosity reported for four genes totaling more than 63 kb of noncoding DNA on the NRY ( ϭ 0.011%) (16), there is 6-7 times more variation on the NRY of chimpanzees and bonobos than on the human NRY. As has been observed with other genetic systems, NRY nucleotide diversity within any single chimpanzee subspecies appears to be the same as (or greater) than the diversity within the entire human species (5,9,19). The contrast between chimpanzees and humans is also apparent in their respective effective population sizes.…”

Section: Discussionsupporting

confidence: 61%

“…They suggested that the lack of intraspecific variation in this intron in humans and great apes is caused by selection acting at the ZFY gene or at a linked site on the NRY. Deinhard and Kidd (19) examined a 940-bp region of the pseudoautosomal boundary region and found three haplotypes in 19 chimpanzees and two haplotypes in 11 bonobos.…”

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confidence: 99%

“…They demonstrated that the three chimpanzee subspecies are characterized by distinct clades of mtDNA hypervariable region I (HVI) haplotypes (3,20). In contrast, haplotypes based on sequences from a 10-kb region on Xq13.3 (9), and the autosomal genes APOB and HOXB6 (19,21), do not show distinct clades defining chimpanzee subspecies, and lineages are often shared between subspecies. By surveying variation on the NRY in these subspecies, we wanted to test whether the phylogenetic structure indicated by mtDNA data reflects a model in which there has been ongoing male gene flow or a model where subspecies have formed recently without subsequent gene flow.…”

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confidence: 99%

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High levels of Y-chromosome nucleotide diversity in the genusPan

Stone

Griffiths

Zegura

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

135

112

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Although some mitochondrial, X chromosome, and autosomal sequence diversity data are available for our closest relatives, Pan troglodytes and Pan paniscus, data from the nonrecombining portion of the Y chromosome (NRY) are more limited. We examined Ϸ3 kb of NRY DNA from 101 chimpanzees, seven bonobos, and 42 humans to investigate: (i) relative levels of intraspecific diversity; (ii) the degree of paternal lineage sorting among species and subspecies of the genus Pan; and (iii) the date of the chimpanzee͞ bonobo divergence. We identified 10 informative sequencetagged sites associated with 23 polymorphisms on the NRY from the genus Pan. Nucleotide diversity was significantly higher on the NRY of chimpanzees and bonobos than on the human NRY. Similar to mtDNA, but unlike X-linked and autosomal loci, lineages defined by mutations on the NRY were not shared among subspecies of P. troglodytes. Comparisons with mtDNA ND2 sequences from some of the same individuals revealed a larger female versus male effective population size for chimpanzees. The NRY-based divergence time between chimpanzees and bonobos was estimated at Ϸ1.8 million years ago. In contrast to human populations who appear to have had a low effective size and a recent origin with subsequent population growth, some taxa within the genus Pan may be characterized by large populations of relatively constant size, more ancient origins, and high levels of subdivision.A great deal has been learned about the evolutionary history of humans and great apes through comparisons of homologous DNA sequences. Humans are thought to be most closely related to chimpanzees (Pan troglodytes) and bonobos (Pan paniscus), with whom we share Ϸ99% of our genomic sequence (1). Much is also being learned about levels of genetic diversity within humans through comparisons of allelic variation at different loci in the human genome (2). Studies of intraspecific diversity in our closest living relatives, however, have lagged far behind those of humans. Comparisons of levels of intraspecific variability have important implications for understanding the processes involved in speciation and clarifying the demographic history of contemporary populations of humans and great apes. Because chimpanzees and bonobos have such a poor fossil record, genetic data can play a major role in elucidating the evolutionary history of the genus Pan.Currently, there are comparative human-chimpanzee sequence data for loci representing three of the four compartments of the genome: the autosomes, the X chromosome, and mtDNA. Comparisons of mitochondrial sequence variation in chimpanzees, bonobos, and humans are consistent in showing 2-to 4-fold higher levels of diversity in both Pan species than in humans (3-6). Studies of autosomal and X-chromosome loci have generally shown higher levels of nucleotide variation in Pan, with some exceptions. In a study of a Ϸ1-kb region of the HOXB6 gene from 105 humans, 45 chimpanzees, and 19 bonobos, Deinard and Kidd (7) found more than three times as much nucleotide diversit...

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Section: Discussionsupporting

confidence: 64%

Section: Discussionsupporting

confidence: 61%

mentioning

confidence: 99%

mentioning

confidence: 99%

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High levels of Y-chromosome nucleotide diversity in the genusPan

Stone

Griffiths

Zegura

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

135

112

View full text Add to dashboard Cite

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“…Analyses of paternally inherited Y-linked genetic markers and maternally inherited mitochondrial DNA markers show that alleles from each subspecies generally form a monophyletic group (Gagneux et al 1999;Stone et al 2002), consistent with lack of hybridization across subspecies. By contrast, autosomal and X-linked markers show intermingling of alleles from different subspecies, a likely result from incomplete lineage sorting and indicative of relatively short separation times (Kaessmann et al 1999;Deinard and Kidd 2000). A three-to fourfold greater effective population size and longer coalescent time for the bisexually transmitted markers than the unisexual markers (Hartl and Clark 1997) can explain the above disparity.…”

Section: Implications and Conclusionmentioning

confidence: 93%

Testing the Chromosomal Speciation Hypothesis for Humans and Chimpanzees

Zhang¹,

Wang²,

Podlaha³

2004

Genome Res.

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Fixed differences of chromosomal rearrangements between isolated populations may promote speciation by preventing between-population gene flow upon secondary contact, either because hybrids suffer from lowered fitness or, more likely, because recombination is reduced in rearranged chromosomal regions. This chromosomal speciation hypothesis thus predicts more rapid genetic divergence on rearranged than on colinear chromosomes because the former are less porous to gene flow. A number of studies of fungi, plants, and animals, including limited genetic data of humans and chimpanzees, support the hypothesis. Here we reexamine the hypothesis for humans and chimpanzees with substantially more genomic data than were used previously. No difference is observed between rearranged and colinear chromosomes in the level of genomic DNA sequence divergence between species. The same is also true for protein sequences. When the gorilla is used as an outgroup, no acceleration in protein sequence evolution associated with chromosomal rearrangements is found. Furthermore, divergence in expression pattern between orthologous genes is not significantly different for rearranged and colinear chromosomes. These results, showing that chromosomal rearrangements did not affect the rate of genetic divergence between humans and chimpanzees, are expected if incipient species on the evolutionary lineages separating humans and chimpanzees did not hybridize.

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Human and Chimpanzee Nucleotide Diversity

Kaessmann

2008

Encyclopedia of Life Sciences

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Nucleotide diversity is a measure of deoxyribonucleic acid (DNA) polymorphism in a population that is based on pairwise DNA sequence comparisons. The extent of nucleotide diversity is shaped by the mutation rate and selection but also by the demographic history of a population. Thus, studies of nucleotide diversity in humans and their closest evolutionary relative, the chimpanzee, shed light on the population history of these species.

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Identifying conservation units within captive chimpanzee populations

Cited by 39 publications

References 61 publications

High levels of Y-chromosome nucleotide diversity in the genusPan

High levels of Y-chromosome nucleotide diversity in the genusPan

Testing the Chromosomal Speciation Hypothesis for Humans and Chimpanzees

Human and Chimpanzee Nucleotide Diversity

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