Genetic and Cultural Kinship among the Lamaleran Whale Hunters

The human ability to form large, coordinated groups is among our most impressive social adaptations. Larger groups facilitate synergistic economies of scale for cooperative breeding, such economic tasks as group hunting, and success in conflict with other groups. In many organisms, genetic relationships provide the structure for sociality to evolve via the process of kin selection, and this is the case, to a certain extent, for humans. But assortment by genetic affiliation is not the only mechanism that can bring people together. Affinity based on symbolically mediated and socially constructed identity, or cultural kinship, structures much of human ultrasociality. This paper examines how genetic kinship and two kinds of cultural kinship--affinal kinship and descent--structure the network of cooperating whale hunters in the village of Lamalera, Indonesia. Social network analyses show that each mechanism of assortment produces characteristic networks of different sizes, each more or less conducive to the task of hunting whales. Assortment via close genetic kin relationships (r?=?0.5) produces a smaller, denser network. Assortment via less-close kin relations (r?=?0.125) produces a larger but less dense network. Affinal networks are small and diffuse; lineage networks are larger, discrete, and very dense. The roles that genetic and cultural kinship play for structuring human sociality is discussed in the context of these results.     

Kinship and Cooperation

Chagnon’s analysis of a well-known axe fight in the Yanomamö village of Mishimishiböwei-teri (Chagnon and Bugos 1979) is among the earliest empirical tests of kin selection theory for explaining cooperation in humans. Kin selection theory describes how cooperation can be organized around genetic kinship and is a fundamental tool for understanding cooperation within family groups. Previous analysis on groups of cooperative Lamaleran whale hunters suggests that the role of genetic kinship as a principle for organizing cooperative human groups could be less important in certain cases than previously thought (Alvard Human Nature 14:129–163, 2003b). Evidence that supports a strong role for genetic kinship—groups are found to be more related than expected by chance—may be spurious because of the correlation between social structure and genetic kinship. Reanalysis of Chagnon’s data using matrix regression techniques, however, confirms that genetic kinship was the primary organizing principle in the axe fight; affinal relations were also important, whereas lineage identity explained nothing.     

The hierarchy of virtue: mutualism, altruism and signaling in Martu women's cooperative hunting

Cooperative hunting is often assumed to be mutualistic, maintained through returns to scale, where, by working together, foragers can gain higher per capita return rates or harvest sizes than they can by hunting alone. We test this hypothesis among Martu hunters and find that cooperation only provides increased returns to poorer hunters while disadvantaging better hunters. Even so, better hunters still cooperate as frequently as poorer hunters. We ask whether better hunters are advantaged in secondary sharing distributions or whether they bias their partner choice to kin or household members. We find that better hunters are not more likely to pair up with kin and they do not gain consumption benefits from acquiring more. They share a greater proportion of their harvest than poorer hunters: no matter how much one produces — better hunter, worse hunter, cooperator, solitary hunter — all eat the same amount in the end. Such a result suggests the hypothesis that cooperation might be a costly signal of commitment to the public interest on the part of better hunters, which generates trust among camp members and facilitates strong social networks, particularly among women, who cooperate more than men. While some foragers may benefit through cooperation from returns to scale or risk reduction, others may benefit more through signaling commitment and generating trust.     

Amplified Fragment Length Polymorphism Fingerprinting Differentiates Genetic Diversity of Xanthomonas oryzae pv. oryzae from Northern Thailand

Thirty isolates of Xanthomonas oryzae pv. oryzae were collected from different rice‐producing area in northern Thailand. For the assessment of genetic variation of bacterial blight pathogen, 19 primer combinations of amplified fragment length polymorphism primer system were screened to evaluate the genetic diversity and five combinations were selected according to their producibility, number of scorable bands and differences detected among representative isolates. Six lineages of X. oryzae pv. oryzae were identified in northern Thailand base on location. Lineage A composed of members from two provinces, Phitsanulok and Chainat. Lineage B was from various provinces as Sukhothai, Phetchaboon, Phicit, Phayao and Phrae. Lineage C was from Phitsanulok and Phrae. Lineage D comprised of members from Phrae, Chiangmai and Chiangrai while the lineage E composed of isolates from Sukhothai and Phitsanulok. The final lineage, lineage F, was from Lampang. Lineages B and D were the most widely distributed while lineage E seemed to be restricted to specific planting area. Wide distribution of the pathogen might be due to seed allocation and germplasm exchanged. Analysis showed that diversity of pathogen is due to single field and cultivars‐specific effects. The results of this study will facilitate the use of effective bacterial blight resistance gene in northern Thailand.     

Agonistic aiding: Kinship,rank, age,and sex influences

An analysis of 3,774 episodes of agonistic aiding collected during a two-year study of a rhesus monkey group (Macaca, mulatta) indicated the differential influence of kinship and rank relationships on the participation of different age-sex classes in both aid to victims and aid to aggressors. Most aiding favored victims rather than aggressors and was much more likely to occur when matrilineal kin were involved. Females were more likely to aid than were males, and the frequency of their participation increased with age. Females were much more influenced by kinship than were males and defended or aggressively supported kin against any third party regardless of dominance relationships. Adult males seldom aided against animals that were dominant to themselves; the rare exceptions occurred when adult males defended kin. Aiding was far more likely to occur if the victim was squealing, and noisy agonistic episodes often involved multiple aiders on both sides. Aiding patterns had some potential to insure dominance rank inheritance within families, in accordance with the Kawamura hypothesis. In aiding animals outside of their own matrilines, however, group members aided randomly with respect to this model. There was little evidence that aiding functioned to support individuals when they targeted animals to which they should be dominant as adults based on matrilineal dominance relationships. Most defensive aiding seemed to function primarily to defend victims (primarily kin) of aggression. Aggressive support of the attacker, on the other hand, seemed to function primarily to reinforce coalitions with the attacker. The identity of the victim was unimportant as long as it was neither kin to nor dominant to the aider. Aggressive support of attackers did not overturn existing dominance relationships.     

OF MICE AND KIN: THE FUNCTIONAL SIGNIFICANCE OF KIN BIAS IN SOCIAL BEHAVIOUR

1. Sharing recent ancestry (kinship) increases the degree of genetic similarity between individuals, where genetic similarity could mean anything from sharing a particular allele to sharing an entire genome. 2. Genetic similarity can influence behavioural and other responses between individuals in a number of ways, discriminatory and non-discriminatory. All are likely to result in kin bias, because of the correlation between genetic similarity and kinship, but only some should be regarded as involving kin discrimination. 3. Non-discriminatory kin bias could arise through close relatives sharing, for instance, physical characteristics (such as those influencing competitive ability), thresholds of behavioural response or requirements for particular resources. 4. Discriminatory kin bias could arise through the direct perception of genetic similarity between individuals (direct similarity discrimination) or the use of cues likely to correlate with genetic similarity (indirect similarity discrimination--of which kin discrimination is one form). Alternatively, it could arise incidentally through mistaken identity or discrimination at some other level, such as species identification. 5. Experiments with laboratory and wild house mice have revealed kin bias in a number of contexts, including (a) parental and infanticidal behaviour, (b) sexual development and behaviour and (c) investigatory behaviour and passive body contact among juveniles and adults. 6. While kin bias in mice has been interpreted as evidence for kin discrimination, there are several problems with such an interpretation. These include (a) pronounced and complex effects of familiarity on discrimination, (b) a high risk of error-proneness in the indirect cues used in apparent kin discrimination and (c) weak and easily disrupted kin bias effects in certain contexts. 7. Consideration of social structure and discriminatory responses within populations of wild house mice leads to an alternative explanation for some kin bias in terms of incidental discrimination based on social group membership. 8. Several results from laboratory experiments suggest incidental discrimination is a more parsimonious explanation than kin discrimination for some intrasexual kin bias in behaviour. However, kin or direct similarity discrimination appears to be the most likely explanation for other aspects of intrasexual kin bias and for intersexual kin bias.     

Nuclear microsatellite and mitochondrial DNA analyses reveal the regional genetic structure and phylogeographical history of a sanguivorous land leech,Haemadipsa japonica,in Japan

Recent molecular studies have indicated that phylogeographical history of Japanese biota is likely shaped by geohistory along with biological events, such as distribution shifts, isolation, and divergence of populations. However, the genetic structure and phylogeographical history of terrestrial Annelida species, including leech species, are poorly understood. Therefore, we aimed to understand the genetic structure and phylogeographical history across the natural range of Haemadipsa japonica, a sanguivorous land leech species endemic to Japan, by using nine polymorphic nuclear microsatellites (nSSR) and cytochrome oxidase subunit one (COI) sequences of mitochondrial DNA (mtDNA). Analyses using nSSR revealed that H. japonica exhibited a stronger regional genetic differentiation among populations (G'_ST = 0.77) than other animal species, probably because of the low mobility of land leech. Analyses using mtDNA indicated that H. japonica exhibited two distinct lineages (A and B), which were estimated to have diverged in the middle Pleistocene and probably because of range fragmentation resulting from climatic change and glacial and interglacial cycles. Lineage A was widely distributed across Japan, and lineage B was found in southwestern Japan. Analyses using nSSR revealed that lineage A was roughly divided into two population groups (i.e., northeastern and southwestern Japan); these analyses also revealed a gradual decrease in genetic diversity with increasing latitude in lineage A and a strong genetic drift in populations of northeastern Japan. Combined with the largely unresolved shallow polytomies from the mtDNA phylogeny, these results implied that lineage A may have undergone a rapid northward migration, probably during the Holocene. Then, the regional genetic structure with local unique gene pools may have been formed within each lineage because of the low mobility of this leech species.     

Food sharing at meals

The presence of a kinship link between nuclear families is the strongest predictor of interhousehold sharing in an indigenous, predominantly Dolgan food-sharing network in northern Russia. Attributes such as the summed number of hunters in paired households also account for much of the variation in sharing between nuclear families. Differences in the number of hunters in partner households, as well as proximity and producer/consumer ratios of households, were investigated with regard to cost-benefit models. The subset of households involved in reciprocal meal sharing is 26 of 84 household host-guest pairs. The frequency of reciprocal meal sharing between families in this subset is positively correlated with average household relatedness. The evolution of cooperation through clustering may illuminate the relationship between kinship and reciprocity at this most intimate level of food sharing.     

Genetic conflict,kin and the origins of novel genetic systems

Genetic conflict may have played an important role in the evolution of novel genetic systems. The ancestral system of eumendelian genetics is highly symmetrical. Those derived from it (e.g. thelytokous parthenogenesis, haplodiploidy and parent-specific allele expression) are more asymmetrical in the genetic role played by maternal versus paternal alleles. These asymmetries may have arisen from maternal–paternal genetic conflict, or cytonuclear conflict, or from an interaction between them. Asymmetric genetic systems are much more common in terrestrial and freshwater taxa than in marine taxa. We suggest three reasons for this, based on the relative inhospitability of terrestrial environments to three types of organism: (i) pathogens—departure from the marine realm meant escape from many pathogens and parasites, reducing the need for sexual reproduction; (ii) symbionts—symbionts are no more important in the terrestrial realm than the marine realm but are more likely to be obligately intracellular and vertically transmitted, making them more likely to disrupt their host''s genetic systems; (iii) Gametes and embryos—because neither gametes nor embryos can be shed into air as easily as into seawater, the mother''s body is a more important environment for both types of organisms in the terrestrial realm than in the marine realm. This environment of asymmetric kinship (with neighbours more closely related by maternal alleles than by paternal alleles) may have helped to drive asymmetries in expression and transmission.     

Genetic diversity and population structure of wintering Western Sandpipers from the Sinaloa coast,Mexico

ABSTRACT Although Western Sandpipers (Calidris mauri) are one of the best‐studied shorebirds along the Pacific Flyway, their genetic identity and population structure is poorly known. We studied the genetic population structure of nonbreeding Western Sandpipers at Bahia Santa María in Sinaloa, northwestern Mexico. A 685‐bp fragment of the mtDNA control region was sequenced for 162 individuals, resulting in 29 variable positions that defined 41 haplotypes. The most common haplotype (WESA01) occurred in 44% of all individuals, whereas 15 were unique to single individuals. Nucleotide diversity was low (π= 0.0030 ± 0.0019 [SE]), but haplotype diversity was moderately high (h= 0.802 ± 0.033 [SE]). The main two maternal lineages exhibited a slightly different local scale distribution that appeared to be related to migratory chronology. Lineage A represented 71% of the haplotypes and was evenly distributed across the nonbreeding season and habitat types, whereas Lineage B represented only 29% of the haplotypes and was disproportionately represented in January in some habitat types. Overall, the low level of nucleotide diversity, the star‐shape of the haplotype tree, the mismatch distribution, and the significantly negative Tajima's D values suggest that Western Sandpipers underwent a recent demographic expansion. Although our results are based on a small sample size from one of several wintering sites along the Pacific Flyway, Santa María likely contains a relatively high proportion of the species genetic variability because it is the wintering ground of nearly 10% of the global population.     

Prevalence of Myxobolus cerebralis infections among genetic lineages of Tubifex tubifex at three locations in the Madison River, Montana

Host biodiversity can impact disease risk and influence the transmission of parasitic disease. Stream sediment-dwelling worms, Tubifex tubifex (Clitellata: Oligochaeta), are the definitive host of the parasite Myxobolus cerebralis (Myxozoa: Myxosporea), which causes whirling disease in salmonid fishes. Genetic diversity of T. tubifex is correlated with host susceptibility to M. cerebralis , and mitochondrial Lineage III is generally shown to be more likely to be infected and produce the triactinomyxon (TAM) spores than other lineages. We determined the mitochondrial lineage, relative abundance, and prevalence of infection of T. tubifex collected at 3 sites in the Madison River, Montana, where previous study had shown variation in whirling disease prevalence and severity in caged trout fry. We also compared visual identification of TAMs released from cultured worms with a molecular genetic assay (diagnostic polymerase chain reaction [PCR]) for parasite detection of both infected and uninfected worms. We estimated that mitochondrial Lineage III was most abundant at the site previously shown to have high fish disease and was also most likely to be infected. The 2 techniques for detecting parasite infection did not always agree, and the likelihood of PCR (+) and spore (-) was not significantly different from PCR (-) and spore (+). Differences in the relative infection prevalence for these 2 lineages may explain the wide range of infection in natural streams.     

Distribution of Fitness in Populations of Dengue Viruses

Genetically diverse RNA viruses like dengue viruses (DENVs) segregate into multiple, genetically distinct, lineages that temporally arise and disappear on a regular basis. Lineage turnover may occur through multiple processes such as, stochastic or due to variations in fitness. To determine the variation of fitness, we measured the distribution of fitness within DENV populations and correlated it with lineage extinction and replacement. The fitness of most members within a population proved lower than the aggregate fitness of populations from which they were drawn, but lineage replacement events were not associated with changes in the distribution of fitness. These data provide insights into variations in fitness of DENV populations, extending our understanding of the complexity between members of individual populations.     

Mitochondrial Diversity and Phylogeographic Patterns of Gekko gecko(Squamata: Gekkonidae) in Thailand

The Tokay Gecko, Gekko gecko(Linnaeus, 1758) is widely distributed in Asia and there have been concerns regarding locally decreasing populations due to overexploitation for traditional Chinese medicine. Previous studies of the genetic relationships of G. gecko populations included few populations from Thailand. Here we investigated the phylogeographic patterns of G. gecko from different regions in Thailand using mitochondrial cytochrome b sequences. Phylogenetic analyses revealed two lineages: one(Lineage A) comprising populations from Laos, Vietnam, and Thailand; and a second(Lineage B) comprising three genetically distinct groups within Thailand alone. Some Thai populations were found to have both lineages represented within them. Highly significant genetic differentiation(FST) showed geographic population structuring in Lineage B, indicating limited gene flow among groups in Thailand. Although G. gecko has a wide distribution and is well adapted to human habitation, the observed genetic structure could potentially be explained by geographic barriers such as mountain ranges. In Lineage A, our study provided primary phylogeographic evidence for lineage mixture that might be a result of human-mediated transport. Future research should include more extensive sampling across the geographic distribution of G. gecko and a landscape genetics approach could be applied for conservation planning.     

A marine fish follows Wallace's Line: the phylogeography of the three-spot seahorse (Hippocampus trimaculatus, Syngnathidae, Teleostei) in Southeast Asia

Aim To test the potential of two contrasting biogeographical hypotheses (‘Indian/Pacific Ocean Basin’ vs. ‘Wallace's Line’) to explain the distribution of genetic diversity among populations of a marine fish in Southeast Asia. Location The marine waters of Asia and Southeast Asia: from India to Japan, and east to the Indonesian islands of Sulawesi and Flores. Methods We sequenced a 696 base pair fragment of cytochrome b DNA of 100 individuals of Hippocampus trimaculatus Leach 1814 (three‐spot seahorse), obtained from across its range. We tested our hypotheses using phylogenetic reconstructions and analyses of molecular variance. Results Significant genetic divergence was observed among the specimens. Two distinct lineages emerged that diverged by an average of 2.9%. The genetic split was geographically associated, but surprisingly it indicated a major east–west division similar to the terrestrial Wallace's Line (Φ_ST = 0.662, P < 0.001) rather than one consistent with an Indian‐Pacific ocean basin separation hypothesis (Φ_ST = 0.023, P = 0.153). Samples from east of Wallace's Line, when analysed separately, however, were consistent with an Indian/Pacific Ocean separation (Φ_ST = 0.461, P = 0.005). The degree of genetic and geographical structure within each lineage also varied. Lineage A, to the west, was evolutionarily shallow (star‐like), and the haplotypes it contained often occurred over a wide area. Lineage B to the east had greater genetic structure, and there was also some evidence of geographical localization of sublineages within B. Main conclusions Our results indicate that the genetic diversity of marine organisms in Southeast Asia may reflect a more complex history than the simple division between two major ocean basins that has been proposed by previous authors. In particular, the east–west genetic division observed here is novel among marine organisms examined to date. The high haplotype, but low nucleotide diversity to the west of Wallace's Line is consistent with post‐glacial colonization of the Sunda Shelf. Additional data are needed to test the generality of these patterns.     

A mathematical approach to multiple genetic relationships

A fundamental concept in the treatment of genetic relationships is that of gene identity which first was introduced by Cotterman (1940). Based on this notion several measures of relationship evolved such as the inbreeding coefficient, the coefficient of kinship, and the identity coefficients; by means of these quantities joint and conditional phenotype probabilities could be derived. This paper is an attempt at a general mathematical treatment of genetic relationships: Identity states are defined for any number of individuals, a method is given for the calculation of the corresponding identity coefficients by means of generalized coefficients of kinship, and applications are emphasized.     

Kinship shapes affiliative social networks but not aggression in ring-tailed coatis

Animal groups typically contain individuals with varying degrees of genetic relatedness, and this variation in kinship has a major influence on patterns of aggression and affiliative behaviors. This link between kinship and social behavior underlies socioecological models which have been developed to explain how and why different types of animal societies evolve. We tested if kinship and age-sex class homophily in two groups of ring-tailed coatis (Nasua nasua) predicted the network structure of three different social behaviors: 1) association, 2) grooming, and 3) aggression. Each group was studied during two consecutive years, resulting in four group-years available for analysis (total of 65 individuals). Association patterns were heavily influenced by agonistic interactions which typically occurred during feeding competition. Grooming networks were shaped by mother-offspring bonds, female-female social relationships, and a strong social attraction to adult males. Mother-offspring pairs were more likely to associate and groom each other, but relatedness had no effect on patterns of aggressive behavior. Additionally, kinship had little to no effect on coalitionary support during agonistic interactions. Adult females commonly came to the aid of juveniles during fights with other group members, but females often supported juveniles who were not their offspring (57% of coalitionary interactions). These patterns did not conform to predictions from socioecological models.     

First Insights into the Phylogenetic Diversity of Mycobacterium tuberculosis in Nepal

Background

Tuberculosis (TB) is a major public health problem in Nepal. Strain variation in Mycobacterium tuberculosis may influence the outcome of TB infection and disease. To date, the phylogenetic diversity of M. tuberculosis in Nepal is unknown.

Methods and Findings

We analyzed 261 M. tuberculosis isolates recovered from pulmonary TB patients recruited between August 2009 and August 2010 in Nepal. M. tuberculosis lineages were determined by single nucleotide polymorphisms (SNP) typing and spoligotyping. Drug resistance was determined by sequencing the hot spot regions of the relevant target genes. Overall, 164 (62.8%) TB patients were new, and 97 (37.2%) were previously treated. Any drug resistance was detected in 50 (19.2%) isolates, and 16 (6.1%) were multidrug-resistant. The most frequent M. tuberculosis lineage was Lineage 3 (CAS/Delhi) with 106 isolates (40.6%), followed by Lineage 2 (East-Asian lineage, includes Beijing genotype) with 84 isolates (32.2%), Lineage 4 (Euro-American lineage) with 41 (15.7%) isolates, and Lineage 1 (Indo-Oceanic lineage) with 30 isolates (11.5%). Based on spoligotyping, we found 45 different spoligotyping patterns that were previously described. The Beijing (83 isolates, 31.8%) and CAS spoligotype (52, 19.9%) were the dominant spoligotypes. A total of 36 (13.8%) isolates could not be assigned to any known spoligotyping pattern. Lineage 2 was associated with female sex (adjusted odds ratio [aOR] 2.58, 95% confidence interval [95% CI] 1.42–4.67, p = 0.002), and any drug resistance (aOR 2.79; 95% CI 1.43–5.45; p = 0.002). We found no evidence for an association of Lineage 2 with age or BCG vaccination status.

Conclusions

We found a large genetic diversity of M. tuberculosis in Nepal with representation of all four major lineages. Lineages 3 and 2 were dominating. Lineage 2 was associated with clinical characteristics. This study fills an important gap on the map of the M. tuberculosis genetic diversity in the Asian region.     

A worldwide phylogeography of the whiteworm lichens Thamnolia reveals three lineages with distinct habitats and evolutionary histories

Thamnolia is a lichenized fungus with an extremely wide distribution, being encountered in arctic and alpine environments in most continents. In this study, we used molecular markers to investigate the population structure of the fungal symbiont and the associated photosynthetic partner of Thamnolia . By analyzing molecular, morphological, and chemical variation among 253 specimens covering the species distribution range, we revealed the existence of three mycobiont lineages. One lineage (Lineage A) is confined to the tundra region of Siberia and the Aleutian Islands, a second (Lineage B) is found in the high alpine region of the Alps and the Carpathians Mountains, and a third (Lineage C) has a worldwide distribution and covers both the aforementioned ecosystems. Molecular dating analysis indicated that the split of the three lineages is older than the last glacial maximum, but the distribution ranges and the population genetic analyses suggest an influence of last glacial period on the present‐day population structure of each lineage. We found a very low diversity of Lineage B, but a higher and similar one in Lineages A and C. Demographic analyses suggested that Lineage C has its origin in the Northern Hemisphere, possibly Scandinavia, and that it has passed through a bottleneck followed by a recent population expansion. While all three lineages reproduce clonally, recombination tests suggest rare or past recombination in both Lineages A and C. Moreover, our data showed that Lineage C has a comparatively low photobiont specificity, being found associated with four widespread Trebouxia lineages (three of them also shared with other lichens), while Lineages A and B exclusively harbor T. simplex s. lat. Finally, we did not find support for the recognition of taxa in Thamnolia based on either morphological or chemical characters.     

Characterization of the cryptic Escherichia lineages: rapid identification and prevalence

Strains phenotypically indistinguishable from Escherichia coli and belonging to at least five distinct cryptic lineages, named Escherichia clades I to V, that are genetically divergent from E. coli yet members of the genus have been recently found using multi-locus sequence typing (MLST). Very few epidemiological data are available on these strains as their detection by MLST is not suitable for large-scale studies. In this work, we developed a rapid PCR method based on aes and chuA allele-specific amplifications that assigns a strain a cryptic lineage membership. By screening more than 3500 strains with this approach, we show that the cryptic lineages of Escherichia are unlikely to be detected in human faecal samples (2-3% frequency) and even less likely to be isolated from extra-intestinal body sites (< 1% frequency). They are more abundant in animal faeces ranging from 3-8% in non-human mammals to 8-28% in birds. Overall, the strains from the clade V are the most abundant and from the clade II very rare. These results suggest that members of the cryptic clades are unlikely to be of significance to human and health but may influence the use of 'E. coli' as an indicator of water quality.