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1.
Philos Trans R Soc Lond B Biol Sci ; 378(1883): 20220301, 2023 08 14.
Artículo en Inglés | MEDLINE | ID: mdl-37381849

RESUMEN

Reproductive inequality, or reproductive skew, drives natural selection, but has been difficult to assess, particularly for males in species with promiscuous mating and slow life histories, such as bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Although bonobos are often portrayed as more egalitarian than chimpanzees, genetic studies have found high male reproductive skew in bonobos. Here, we discuss mechanisms likely to affect male reproductive skew in Pan, then re-examine skew patterns using paternity data from published work and new data from the Kokolopori Bonobo Reserve, Democratic Republic of Congo and Gombe National Park, Tanzania. Using the multinomial index (M), we found considerable overlap in skew between the species, but the highest skew occurred among bonobos. Additionally, for two of three bonobo communities, but no chimpanzee communities, the highest ranking male had greater siring success than predicted by priority-of-access. Thus, an expanded dataset covering a broader demographic range confirms that bonobos have high male reproductive skew. Detailed comparison of data from Pan highlights that reproductive skew models should consider male-male dynamics including the effect of between-group competition on incentives for reproductive concessions, but also female grouping patterns and factors related to male-female dynamics including the expression of female choice. This article is part of the theme issue 'Evolutionary ecology of inequality'.


Asunto(s)
Pan paniscus , Pan troglodytes , Femenino , Masculino , Animales , Evolución Biológica , Comunicación Celular , Congo
2.
Mol Ecol ; 32(14): 3842-3858, 2023 07.
Artículo en Inglés | MEDLINE | ID: mdl-37277946

RESUMEN

Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south-eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability. To address this uncertainty, we generated both mitochondrial and MiSeq-based microsatellite genotypes for 290 individuals ranging across western Tanzania. While shared mitochondrial haplotypes confirmed historical gene flow, our microsatellite analyses revealed two distinct clusters, suggesting two populations currently isolated from one another. However, we found evidence of high levels of gene flow maintained within each of these clusters, one of which covers an 18,000 km2 ecosystem. Landscape genetic analyses confirmed the presence of barriers to gene flow with rivers and bare habitats highly restricting chimpanzee movement. Our study demonstrates how advances in sequencing technologies, combined with the development of landscape genetics approaches, can resolve ambiguities in the genetic history of critical populations and better inform conservation efforts of endangered species.


Asunto(s)
Variación Genética , Genética de Población , Animales , Variación Genética/genética , Ecosistema , Pan troglodytes/genética , Flujo Génico , Repeticiones de Microsatélite/genética , Haplotipos/genética
3.
Zoo Biol ; 42(5): 668-674, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37151175

RESUMEN

Across zoo's accredited by the Association of Zoos and Aquariums (AZA), species are typically managed as a single population to retain 90% of the founding members' gene diversity. Often, little is known about the specific geographic origins of the founders or how representative the ex situ population's genetic diversity is of the wild population. This study uses mitochondrial DNA (mtDNA) sequencing to investigate haplotype diversity and geographic female founder origin of the AZA-managed Angolan colobus (Colobus angolensis) monkey population. We obtained fecal samples from individuals closely related to founder animals at five zoos and found four haplotypes among 23 individuals. Analyzed together with wild C. angolensis haplotypes, we found two haplotypes identical to those found in Tanzanian populations: one haplotype, possessed by 13 individuals (descended from three founders), matched an East Usambara Mountains haplotype, while the other, possessed by seven individuals (from four founders), matched a haplotype found in both the South Pare Mountains and Rufiji River. Two haplotypes were not detected in wild populations but were closely related to haplotypes found in the Rufiji River (one individual descended from one founder) and Shimoni, Kenya (two individuals descended from one founder) populations, suggesting nearby origins. Thus, the AZA-managed population of Angolan colobus likely originated from several localities, but all have mtDNA lineages associated with the subspecies C. a. palliatus, a Vulnerable subspecies. Examining founders' mtDNA haplotypes may be a useful addition to the zoo population management toolkit to help improve breeding recommendations by identifying individuals with rare haplotypes and revealing likely kinship among founders.


Asunto(s)
Animales de Zoológico , Colobus , Humanos , Femenino , Animales , Colobus/genética , Animales de Zoológico/genética , ADN Mitocondrial/genética , Haplotipos , Variación Genética
4.
Proc Natl Acad Sci U S A ; 120(22): e2220124120, 2023 05 30.
Artículo en Inglés | MEDLINE | ID: mdl-37216525

RESUMEN

To address claims of human exceptionalism, we determine where humans fit within the greater mammalian distribution of reproductive inequality. We show that humans exhibit lower reproductive skew (i.e., inequality in the number of surviving offspring) among males and smaller sex differences in reproductive skew than most other mammals, while nevertheless falling within the mammalian range. Additionally, female reproductive skew is higher in polygynous human populations than in polygynous nonhumans mammals on average. This patterning of skew can be attributed in part to the prevalence of monogamy in humans compared to the predominance of polygyny in nonhuman mammals, to the limited degree of polygyny in the human societies that practice it, and to the importance of unequally held rival resources to women's fitness. The muted reproductive inequality observed in humans appears to be linked to several unusual characteristics of our species-including high levels of cooperation among males, high dependence on unequally held rival resources, complementarities between maternal and paternal investment, as well as social and legal institutions that enforce monogamous norms.


Asunto(s)
Reproducción , Caracteres Sexuales , Animales , Humanos , Femenino , Masculino , Matrimonio , Mamíferos , Conducta Sexual Animal
5.
Nat Commun ; 14(1): 1033, 2023 02 23.
Artículo en Inglés | MEDLINE | ID: mdl-36823144

RESUMEN

The malaria parasite Plasmodium falciparum causes substantial human mortality, primarily in equatorial Africa. Enriched in affected African populations, the B*53 variant of HLA-B, a cell surface protein that presents peptide antigens to cytotoxic lymphocytes, confers protection against severe malaria. Gorilla, chimpanzee, and bonobo are humans' closest living relatives. These African apes have HLA-B orthologs and are infected by parasites in the same subgenus (Laverania) as P. falciparum, but the consequences of these infections are unclear. Laverania parasites infect bonobos (Pan paniscus) at only one (TL2) of many sites sampled across their range. TL2 spans the Lomami River and has genetically divergent subpopulations of bonobos on each side. Papa-B, the bonobo ortholog of HLA-B, includes variants having a B*53-like (B07) peptide-binding supertype profile. Here we show that B07 Papa-B occur at high frequency in TL2 bonobos and that malaria appears to have independently selected for different B07 alleles in the two subpopulations.


Asunto(s)
Antígenos de Histocompatibilidad Clase I , Malaria Falciparum , Pan paniscus , Plasmodium , Animales , Malaria Falciparum/genética , Pan paniscus/genética , Pan paniscus/parasitología , Péptidos , Filogenia , Antígenos de Histocompatibilidad Clase I/genética
6.
Am J Primatol ; 84(7): e23384, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35389522

RESUMEN

Whether the Colobus angolensis that reside in the fragmented forests in eastern Kenya and Tanzania represent one subspecies or two has been debated for 50 years. Morphological and more recent genetic and ecological studies suggest that these populations represent two subspecies, C. a. palliatus and C. a. sharpei. However, their distribution of mitochondrial variation remains unresolved since the genetic study only characterized four populations at the range ends. Therefore, we characterized five populations in the area of the hypothesized subspecies divide. We identified eight new haplotypes which, combined with those previously identified, provided 26 haplotypes from nine populations for analysis. Haplotypes found south of the Rufiji River cluster together but separately from northern haplotypes. The largest sequence differences within cytochrome b occur between population pairs representing opposite sides of the river; their mean difference (1.5%) is more than that of other primate subspecies. Analysis of molecular variance attributes most of the variation to that north versus south of the river. These results support the previous subspecies distinction between C. a. palliatus (northern) and C. a. sharpei (southern), divided by the Rufiji River. The estimated time of the most recent common ancestor of all haplotypes indicates that the subspecies have been isolated from each other for approximately 550,000 years. The common ancestor of northern and southern haplogroups was 370,000 and 290,000 years ago, respectively. Nevertheless, the correlation between genetic and geographic distances suggests that isolation-by-distance contributed to population structuring. Significant variation among populations, with only three haplotypes shared between populations, also indicates that an extended period of isolation drove population distinctiveness. Considering these results, we evaluate hypotheses about the founding and differentiation of these subspecies during Pleistocene climatic fluctuations and propose a novel, more direct migration route from Central Africa to their current range navigating Lake Tanganyika, the central Tanzanian corridor, and the Rufiji River.


Asunto(s)
Colobus , Bosques , Animales , Colobus/genética , ADN Mitocondrial/genética , Variación Genética , Haplorrinos , Haplotipos , Kenia , Filogenia , Tanzanía
7.
J Hum Evol ; 144: 102795, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32454364

RESUMEN

Across vertebrates, species with intense male mating competition and high levels of sexual dimorphism in body size generally exhibit dimorphism in age-specific fertility. Compared with females, males show later ages at first reproduction and earlier reproductive senescence because they take longer to attain adult body size and musculature, and maintain peak condition for a limited time. This normally yields a shorter male duration of effective breeding, but this reduction might be attenuated in species that frequently use coalitionary aggression. Here, we present comparative genetic and demographic data on chimpanzees from three long-term study communities (Kanyawara: Kibale National Park, Uganda; Mitumba and Kasekela: Gombe National Park, Tanzania), comprising 581 male risk years and 112 infants, to characterize male age-specific fertility. For comparison, we update estimates from female chimpanzees in the same sites and append a sample of human foragers (the Tanzanian Hadza). Consistent with the idea that aggressive mating competition favors youth, chimpanzee males attained a higher maximum fertility than females, followed by a steeper decline with age. Males did not show a delay in reproduction compared with females, however, as adolescents in both sites successfully reproduced by targeting young, subfecund females, who were less attractive to adults. Gombe males showed earlier reproductive senescence and a shorter duration of effective breeding than Gombe females. By contrast, older males in Kanyawara generally continued to reproduce, apparently by forming coalitions with the alpha. Hadza foragers showed a distinct pattern of sexual dimorphism in age-specific fertility as, compared with women, men gained conceptions later but continued reproducing longer. In sum, both humans and chimpanzees showed sexual dimorphism in age-specific fertility that deviated from predictions drawn from primates with more extreme body size dimorphism, suggesting altered dynamics of male-male competition in the two lineages. In both species, coalitions appear important for extending male reproductive careers.


Asunto(s)
Fertilidad , Pan troglodytes/fisiología , Caracteres Sexuales , Factores de Edad , Animales , Femenino , Humanos , Masculino , Tanzanía
8.
Immunogenetics ; 72(1-2): 25-36, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31624862

RESUMEN

The major histocompatibility complex (MHC) is central to the innate and adaptive immune responses of jawed vertebrates. Characteristic of the MHC are high gene density, gene copy number variation, and allelic polymorphism. Because apes and monkeys are the closest living relatives of humans, the MHCs of these non-human primates (NHP) are studied in depth in the context of evolution, biomedicine, and conservation biology. The Immuno Polymorphism Database (IPD)-MHC NHP Database (IPD-MHC NHP), which curates MHC data of great and small apes, as well as Old and New World monkeys, has been upgraded. The curators of the database are responsible for providing official designations for newly discovered alleles. This nomenclature report updates the 2012 report, and summarizes important nomenclature issues and relevant novel features of the IPD-MHC NHP Database.


Asunto(s)
Bases de Datos Genéticas , Complejo Mayor de Histocompatibilidad/genética , Primates/genética , Primates/inmunología , Alelos , Animales , Cercopithecidae/genética , Hominidae/genética , Complejo Mayor de Histocompatibilidad/fisiología , Filogenia , Platirrinos/genética , Polimorfismo Genético , Terminología como Asunto
9.
Immunogenetics ; 72(1-2): 131-132, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31745605

RESUMEN

The original version of this article contained a spelling error in the Acknowledgments regarding the name of the funding organisation supporting GM and JAH. UKRI-BBSCR should have been UKRI-BBSRC, as is now indicated correctly below.

10.
Curr Biol ; 29(10): R354-R355, 2019 05 20.
Artículo en Inglés | MEDLINE | ID: mdl-31112681

RESUMEN

In many group-living mammals, mothers may increase the reproductive success of their daughters even after they are nutritionally independent and fully grown [1]. However, whether such maternal effects exist for adult sons is largely unknown. Here we show that males have higher paternity success when their mother is living in the group at the time of the offspring's conception in bonobos (N = 39 paternities from 4 groups) but not in chimpanzees (N = 263 paternities from 7 groups). These results are consistent with previous research showing a stronger role of mothers (and females more generally) in bonobo than chimpanzee societies.


Asunto(s)
Madres , Pan paniscus/fisiología , Pan troglodytes/fisiología , Paternidad , Conducta Sexual Animal , Animales , Femenino , Masculino , Especificidad de la Especie
11.
Front Immunol ; 10: 177, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-30837985

RESUMEN

Natural killer (NK) cells have diverse roles in hominid immunity and reproduction. Modulating these functions are the interactions between major histocompatibility complex (MHC) class I molecules that are ligands for two NK cell surface receptor types. Diverse killer cell immunoglobulin-like receptors (KIR) bind specific motifs encoded within the polymorphic MHC class I cell surface glycoproteins, while, in more conserved interactions, CD94:NKG2A receptors recognize MHC-E with bound peptides derived from MHC class I leader sequences. The hominid lineage presents a choreographed co-evolution of KIR with their MHC class I ligands. MHC-A, -B, and -C are present in all great apes with species-specific haplotypic variation in gene content. The Bw4 epitope recognized by lineage II KIR is restricted to MHC-B but also present on some gorilla and human MHC-A. Common to great apes, but rare in humans, are MHC-B possessing a C1 epitope recognized by lineage III KIR. MHC-C arose from duplication of MHC-B and is fixed in all great apes except orangutan, where it exists on approximately 50% of haplotypes and all allotypes are C1-bearing. Recent study showed that gorillas possess yet another intermediate MHC organization compared to humans. Like orangutans, but unlike the Pan-Homo species, duplication of MHC-B occurred. However, MHC-C is fixed, and the MHC-C C2 epitope (absent in orangutans) emerges. The evolution of MHC-C drove expansion of its cognate lineage III KIR. Recently, position -21 of the MHC-B leader sequence has been shown to be critical in determining NK cell educational outcome. In humans, methionine (-21M) results in CD94:NKG2A-focused education whereas threonine (-21T) produces KIR-focused education. This is another dynamic position among hominids. Orangutans have exclusively -21M, consistent with their intermediate stage in lineage III KIR-focused evolution. Gorillas have both -21M and -21T, like humans, but they are unequally encoded by their duplicated B genes. Chimpanzees have near-fixed -21T, indicative of KIR-focused NK education. Harmonious with this observation, chimpanzee KIR exhibit strong binding and, compared to humans, smaller differences between binding levels of activating and inhibitory KIR. Consistent between these MHC-NK cell receptor systems over the course of hominid evolution is the evolution of polymorphism favoring the more novel and dynamic KIR system.


Asunto(s)
Evolución Biológica , Antígenos de Histocompatibilidad/inmunología , Células Asesinas Naturales/inmunología , Células Asesinas Naturales/metabolismo , Receptores de Células Asesinas Naturales/metabolismo , Alelos , Animales , Evolución Molecular , Duplicación de Gen , Haplotipos , Antígenos de Histocompatibilidad/química , Antígenos de Histocompatibilidad/genética , Hominidae/clasificación , Hominidae/fisiología , Humanos , Ligandos , Filogenia , Polimorfismo Genético , Unión Proteica , Señales de Clasificación de Proteína , Receptores de Células Asesinas Naturales/química , Receptores de Células Asesinas Naturales/genética , Reproducción/genética
12.
Ecol Evol ; 8(16): 7946-7963, 2018 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-30250675

RESUMEN

Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.

13.
Genome Res ; 27(5): 813-823, 2017 05.
Artículo en Inglés | MEDLINE | ID: mdl-28360230

RESUMEN

The most polymorphic part of the human genome, the MHC, encodes over 160 proteins of diverse function. Half of them, including the HLA class I and II genes, are directly involved in immune responses. Consequently, the MHC region strongly associates with numerous diseases and clinical therapies. Notoriously, the MHC region has been intractable to high-throughput analysis at complete sequence resolution, and current reference haplotypes are inadequate for large-scale studies. To address these challenges, we developed a method that specifically captures and sequences the 4.8-Mbp MHC region from genomic DNA. For 95 MHC homozygous cell lines we assembled, de novo, a set of high-fidelity contigs and a sequence scaffold, representing a mean 98% of the target region. Included are six alternative MHC reference sequences of the human genome that we completed and refined. Characterization of the sequence and structural diversity of the MHC region shows the approach accurately determines the sequences of the highly polymorphic HLA class I and HLA class II genes and the complex structural diversity of complement factor C4A/C4B It has also uncovered extensive and unexpected diversity in other MHC genes; an example is MUC22, which encodes a lung mucin and exhibits more coding sequence alleles than any HLA class I or II gene studied here. More than 60% of the coding sequence alleles analyzed were previously uncharacterized. We have created a substantial database of robust reference MHC haplotype sequences that will enable future population scale studies of this complicated and clinically important region of the human genome.


Asunto(s)
Complemento C4/genética , Genes MHC Clase II , Genes MHC Clase I , Haplotipos , Mucinas/genética , Polimorfismo Genético , Animales , Línea Celular , Mapeo Contig/métodos , Mapeo Contig/normas , Genoma Humano , Genómica/métodos , Genómica/normas , Humanos , Sistemas de Lectura Abierta , Pan troglodytes/genética , Estándares de Referencia
14.
R Soc Open Sci ; 4(1): 160422, 2017 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-28280546

RESUMEN

Inbreeding adversely affects fitness, whereas heterozygosity often augments it. Therefore, mechanisms to avoid inbreeding and increase genetic distance between mates should be advantageous in species where adult relatives reside together. Here we investigate mate choice for genetic dissimilarity in chimpanzees, a species in which many females avoid inbreeding through dispersal, but where promiscuous mating and sexual coercion can limit choice when related adults reside together. We take advantage of incomplete female dispersal in Gombe National Park, Tanzania to compare mate choice for genetic dissimilarity among immigrant and natal females in two communities using pairwise relatedness measures in 135 genotyped chimpanzees. As expected, natal females were more related to adult males in their community than were immigrant females. However, among 62 breeding events, natal females were not more related to the sires of their offspring than immigrant females, despite four instances of close inbreeding. Moreover, females were generally less related to the sires of their offspring than to non-sires. These results demonstrate that chimpanzees may be capable of detecting relatedness and selecting mates on the basis of genetic distance.

15.
J Immunol ; 198(9): 3480-3493, 2017 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-28348269

RESUMEN

Fast-evolving MHC class I polymorphism serves to diversify NK cell and CD8 T cell responses in individuals, families, and populations. Because only chimpanzee and bonobo have strict orthologs of all HLA class I, their study gives unique perspectives on the human condition. We defined polymorphism of Papa-B, the bonobo ortholog of HLA-B, for six wild bonobo populations. Sequences for Papa-B exon 2 and 3 were determined from the genomic DNA in 255 fecal samples, minimally representing 110 individuals. Twenty-two Papa-B alleles were defined, each encoding a different Papa-B protein. No Papa-B is identical to any chimpanzee Patr-B, human HLA-B, or gorilla Gogo-B. Phylogenetic analysis identified a clade of MHC-B, defined by residues 45-74 of the α1 domain, which is broadly conserved among bonobo, chimpanzee, and gorilla. Bonobo populations have 3-14 Papa-B allotypes. Three Papa-B are in all populations, and they are each of a different functional type: allotypes having the Bw4 epitope recognized by killer cell Ig-like receptors of NK cells, allotypes having the C1 epitope also recognized by killer cell Ig-like receptors, and allotypes having neither epitope. For population Malebo, these three Papa-B are the only Papa-B allotypes. Although small in number, their sequence divergence is such that the nucleotide diversity (mean proportional distance) of Papa-B in Malebo is greater than in the other populations and is also greater than expected for random combinations of three Papa-B Overall, Papa-B has substantially less diversity than Patr-B in chimpanzee subspecies and HLA-B in indigenous human populations, consistent with bonobo having experienced narrower population bottlenecks.


Asunto(s)
Antígenos de Histocompatibilidad Clase I/genética , Sistema Inmunológico , Epítopos Inmunodominantes/genética , Células Asesinas Naturales/inmunología , Pan paniscus , Animales , Evolución Biológica , Frecuencia de los Genes , Genotipo , Gorilla gorilla , Antígenos HLA-B/genética , Humanos , Pan troglodytes , Filogenia , Polimorfismo Genético
16.
R Soc Open Sci ; 3(11): 160441, 2016 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-28018626

RESUMEN

Promiscuous mating was traditionally thought to curtail paternal investment owing to the potential costs of providing care to unrelated infants. However, mounting evidence suggests that males in some promiscuous species can recognize offspring. In primates, evidence for paternal care exists in promiscuous Cercopithecines, but less is known about these patterns in other taxa. Here, we examine two hypotheses for paternal associations with lactating mothers in eastern chimpanzees (Pan troglodytes schweinfurthii): paternal effort, whereby males associate and interact more with their own infants, and mating effort, whereby males invest in mothers and offspring for mating privileges. We found that fathers associated more with their offspring than they did with non-kin infants, particularly early in life when infanticide risk is highest. Additionally, fathers and their infant offspring interacted more than expected. Notably, association between fathers and mother-infant pairs did not predict the probability of siring the mother's next offspring. Our results support the paternal effort, but not the mating effort hypothesis in this species. Chimpanzees are one of the most salient models for the last common ancestor between Pan and Homo, thus our results suggest that a capacity for paternal care, possibly independent of long-term mother-father bonds, existed early in hominin evolution.

17.
Am J Hum Genet ; 99(2): 375-91, 2016 Aug 04.
Artículo en Inglés | MEDLINE | ID: mdl-27486779

RESUMEN

The physiological functions of natural killer (NK) cells in human immunity and reproduction depend upon diverse interactions between killer cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands: HLA-A, HLA-B, and HLA-C. The genomic regions containing the KIR and HLA class I genes are unlinked, structurally complex, and highly polymorphic. They are also strongly associated with a wide spectrum of diseases, including infections, autoimmune disorders, cancers, and pregnancy disorders, as well as the efficacy of transplantation and other immunotherapies. To facilitate study of these extraordinary genes, we developed a method that captures, sequences, and analyzes the 13 KIR genes and HLA-A, HLA-B, and HLA-C from genomic DNA. We also devised a bioinformatics pipeline that attributes sequencing reads to specific KIR genes, determines copy number by read depth, and calls high-resolution genotypes for each KIR gene. We validated this method by using DNA from well-characterized cell lines, comparing it to established methods of HLA and KIR genotyping, and determining KIR genotypes from 1000 Genomes sequence data. This identified 116 previously uncharacterized KIR alleles, which were all demonstrated to be authentic by sequencing from source DNA via standard methods. Analysis of just two KIR genes showed that 22% of the 1000 Genomes individuals have a previously uncharacterized allele or a structural variant. The method we describe is suited to the large-scale analyses that are needed for characterizing human populations and defining the precise HLA and KIR factors associated with disease. The methods are applicable to other highly polymorphic genes.


Asunto(s)
Genes MHC Clase I/genética , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Receptores KIR/genética , Alelos , Dosificación de Gen , Genoma Humano/genética , Antígenos HLA-A/genética , Antígenos HLA-B/genética , Antígenos HLA-C/genética , Haplotipos , Humanos , Polimorfismo Genético
18.
PLoS Biol ; 13(5): e1002144, 2015 May.
Artículo en Inglés | MEDLINE | ID: mdl-26020813

RESUMEN

Major histocompatibility complex (MHC) class I molecules determine immune responses to viral infections. These polymorphic cell-surface glycoproteins bind peptide antigens, forming ligands for cytotoxic T and natural killer cell receptors. Under pressure from rapidly evolving viruses, hominoid MHC class I molecules also evolve rapidly, becoming diverse and species-specific. Little is known of the impact of infectious disease epidemics on MHC class I variant distributions in human populations, a context in which the chimpanzee is the superior animal model. Population dynamics of the chimpanzees inhabiting Gombe National Park, Tanzania have been studied for over 50 years. This population is infected with SIVcpz, the precursor of human HIV-1. Because HLA-B is the most polymorphic human MHC class I molecule and correlates strongly with HIV-1 progression, we determined sequences for its ortholog, Patr-B, in 125 Gombe chimpanzees. Eleven Patr-B variants were defined, as were their frequencies in Gombe's three communities, changes in frequency with time, and effect of SIVcpz infection. The growing populations of the northern and central communities, where SIVcpz is less prevalent, have stable distributions comprising a majority of low-frequency Patr-B variants and a few high-frequency variants. Driving the latter to high frequency has been the fecundity of immigrants to the northern community, whereas in the central community, it has been the fecundity of socially dominant individuals. In the declining population of the southern community, where greater SIVcpz prevalence is associated with mortality and emigration, Patr-B variant distributions have been changing. Enriched in this community are Patr-B variants that engage with natural killer cell receptors. Elevated among SIVcpz-infected chimpanzees, the Patr-B*06:03 variant has striking structural and functional similarities to HLA-B*57, the human allotype most strongly associated with delayed HIV-1 progression. Like HLA-B*57, Patr-B*06:03 correlates with reduced viral load, as assessed by detection of SIVcpz RNA in feces.


Asunto(s)
Genes MHC Clase I , Pan troglodytes/inmunología , Virus de la Inmunodeficiencia de los Simios/inmunología , Alelos , Animales , ADN/análisis , Heces/química , Femenino , Aptitud Genética , Variación Genética , Masculino , Pan troglodytes/genética , Reproducción
19.
Curr Biol ; 24(23): 2855-60, 2014 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-25454788

RESUMEN

In sexually reproducing animals, male and female reproductive strategies often conflict. In some species, males use aggression to overcome female choice, but debate persists over the extent to which this strategy is successful. Previous studies of male aggression toward females among wild chimpanzees have yielded contradictory results about the relationship between aggression and mating behavior. Critically, however, copulation frequency in primates is not always predictive of reproductive success. We analyzed a 17-year sample of behavioral and genetic data from the Kasekela chimpanzee (Pan troglodytes schweinfurthii) community in Gombe National Park, Tanzania, to test the hypothesis that male aggression toward females increases male reproductive success. We examined the effect of male aggression toward females during ovarian cycling, including periods when the females were sexually receptive (swollen) and periods when they were not. We found that, after controlling for confounding factors, male aggression during a female's swollen periods was positively correlated with copulation frequency. However, aggression toward swollen females was not predictive of paternity. Instead, aggression by high-ranking males toward females during their nonswollen periods was positively associated with likelihood of paternity. This indicates that long-term patterns of intimidation allow high-ranking males to increase their reproductive success, supporting the sexual coercion hypothesis. To our knowledge, this is the first study to present genetic evidence of sexual coercion as an adaptive strategy in a social mammal.


Asunto(s)
Agresión , Pan troglodytes , Conducta Sexual Animal/fisiología , Animales , Copulación , Femenino , Masculino , Paternidad , Tanzanía
20.
Behav Ecol Sociobiol ; 67(3): 373-381, 2013 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-23459197

RESUMEN

Coalitionary aggression occurs when at least two individuals jointly direct aggression at one or more conspecific targets. Scientists have long argued that this common form of cooperation has positive fitness consequences. Nevertheless, despite evidence that social bond strength (which is thought to promote coalition formation) is correlated with fitness in primates, cetaceans, and ungulates, few studies have directly examined whether coalitionary aggression improves reproductive success. We tested the hypothesis that among free-ranging chimpanzees (Pan troglodytes schweinfurthii), participation in coalitionary aggression increases reproductive output. Using 14 years of genetic and behavioral data from Gombe National Park, Tanzania, we found that coalitionary aggression increased a male's chances of A) siring offspring, compared to other males of similar dominance rank, and B) ascending in rank, a correlate of future reproductive output. Because male chimpanzees form coalitions with many others within a complex network, we used social network analysis to identify the types of connections correlated with these fitness benefits. The beneficiaries of coalitionary aggression were males with the highest 'betweenness' - that is, those who tended to have coalition partners who themselves did not form coalitions with each other. This suggests that beyond simply recognizing third-party relationships, chimpanzees may use this knowledge to choose coalition partners. If so, this is a significant step forward in our knowledge of the adaptive value of social intelligence. Regardless of mechanism, however, this is the first evidence of genetic benefits of coalitionary aggression in this species, and therefore has important implications for understanding the evolution of cooperation.

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