The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

Background: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of singlecopy DNA and have tried to exclude segmental duplications (SDs). This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements. Results: Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. Conclusion: We find that interspecific SD divergence behaves similarly to divergence of singlecopy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.This research was supported by a grant to A.N. from the Ministerio de Ciencia y Tecnologia (Spain, BFU2006 15413-C02-01) and by BE2005 and BP2006 fellowships to T.M.B from the "Departament d'Educacio i Universitats de la Generalitat de Catalunya"

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees

Analysis of the genes located in rearranged human and chimpanzee chromosomes identified lower divergence than for those in colinear chromosomes

Abstract overview of the chromosomal regions that were included and excluded from our analysis

<p><b>Copyright information:</b></p><p>Taken from "On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees"</p><p>http://genomebiology.com/2007/8/10/R230</p><p>Genome Biology 2007;8(10):R230-R230.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2246304.</p><p></p> A colinear and an inverted chromosome are presented. The inversion in the rearranged chromosome is highlighted in red. For every chromosome, regions considered in this paper are labeled in black. Regions excluded from the main analysis (telomeres, centromeres and breakpoints (BKP)) are within boxes and labeled in red

Circular DNA intermediates in the generation of large human segmental duplications

Background: Duplications of large genomic segments provide genetic diversity in genome evolution. Despite their importance, how these duplications are generated remains uncertain, particularly for distant duplicated genomic segments. Results: Here we provide evidence of the participation of circular DNA intermediates in the single generation of some large human segmental duplications. A specific reversion of sequence order from A-B/C-D to B-A/D-C between duplicated segments and the presence of only microhomologies and short indels at the evolutionary breakpoints suggest a circularization of the donor ancestral locus and an accidental replicative interaction with the acceptor locus. Conclusions: This novel mechanism of random genomic mutation could explain several distant genomic duplications including some of the ones that took place during recent human evolution

Morphometric, behavioral, and genomic evidence for a new orangutan species

Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive.This work was financially supported by University of 291 Zurich (UZH) Forschungskredit grants FK-10 (MPMG), FK-15-103 (AlN), and FK-14-094 (TBS), 292 Swiss National Science Foundation grant 3100A-116848 (MK, CvS), Leakey Foundation (MPMG), 293 A.H. Schultz Foundation grants (MK, MPMG), UZH Research Priority Program ‘Evolution in Action’ 294 (MK), the Arcus Foundation (EM), Australian National University (ANU) research fund (AnN), ANU 295 Vice Chancellor Travel Grant (AnN), Australia Awards Scholarship-DFAT (AnN), ERC Starting Grant 296 260372 (TMB), EMBO YIP 2013 (TMB), MINECO BFU2014-55090-P, BFU2015-7116-ERC, 297 BFU2015-6215-ERCU01, and MH106874 (TMB), Fundacio Zoo Barcelona (TMB), Julius–Klaus 298 Foundation (MK), MINECO/FEDER BFU2016-77961-P (JB, MP), Gates Cambridge Trust (TD), and 299 the Department of Anthropology at the University of Zuric