Electronic Supplemental Materials

Electronic Supplemental Materials

Where sociality and relatedness diverge: The genetic basis for hierarchical social organization in African elephants

George Wittemyer, John BA Okello, Henrik B. Rasmussen, Peter Arctander, Silvester Nyakaana, Iain Douglas-Hamilton, and Hans R Siegismund

Correspondence should be addressed to G.W. ()

Methods

Detailed description of genotyped social unit constituents

The 102 breeding females successfully genotyped were member of 47 of the 50 2nd tier groups. Of the original 32 2nd tier groups containing two or more breeding females (18 of the 50 behaviorally defined groups consisted of a single breeding female and her offspring), 29 were used in the analysis of the genetic basis for 2nd tier groups: 26 for which all members were genotyped and three for which sampling was not possible for a single breeding female. Therefore, only three of the total 2nd tier groups were precluded from analysis because of failed genotyping of constituent females. Representation of genotyped individuals was sufficient for analysis of the genetic basis for twelve of the fifteen 3rd tier groups. The complete assemblages of breeding females were genotyped in nine 3rd tier groups and representatives of each component 2nd tier group were complete in three others. The genetic basis for three 3rd tier groups was not analyzed because not all of their component 2nd tier groups were represented. Breeding females representing all eight 4th tier groups were genotyped; however, the structure of three of the eight did not differ from their 3rd tier designation (Wittemyer et al. 2005), so analysis here is focused only on the unique five.

Further details regarding microsatellite and mitochondrial DNA genotyping

The microsatellite loci analyzed are: LaT05, LaT06, LaT07, LaT08, LaT13, LaT16, LaT17, LaT18, LaT24, LaT25, LaT26 (Archie et al. 2003), FH1, FH39, FH40, H67, FH103 (Comstock et al. 2000), LA4, LA6 (Eggert et al. 2000); LafMS02 (Nyakaana & Arctander 1998), and LafMS06 (Nyakaana et al. 2005). Overall, the study adopted a rigid genotyping process that included multiple tubes approach (Taberlet et al. 1996) and parent-offspring Mendelian checks to confirm the compatibility of alleles (Okello et al. 2005). Each individual locus was genotyped at least twice to confirm the genotypes, and for the few inconsistencies, two more repeat genotyping were done with a majority consensus genotype taken (Taberlet et al. 1996). This approach yielded high genotyping success with an approximated genotyping error rate of less than 2% and a low estimated average null allele frequency (0.011) well below that which a previous simulation based study suggested would bias individual based genetic analyses (Dakin & Avise 2004). Genetic variation for the population was estimated from a total of 400 individuals (male and resident and non-resident females) genotyped, representing over 20% of the total Samburu elephant population and 7% of the broader population in the Samburu–Laikipia ecosystem of Kenya. The mean number of alleles per locus was 10.8 (range 5-21) and mean HE was 0.74 (range 0.52-0.90) as summarized previously (Okello et al. 2005).

Both strands of the template mitochondrial DNA were sequenced following the dideoxy chaintermination method of Sanger et al. (1977) with the BigDye terminator cycle sequencing kit (Applied Biosystems), according to the manufacturer’s instructions. The products were electrophoresed using 4% polyacrylamide gels on an ABI 377 prism (Applied Biosystems) and analyzed using the program SEQUENCHER version 4.7 (Gene Codes, USA). The sequences were assembled in BIOEDIT 7.0.5 (Hall 1999), and automatically aligned using CLUTSTAL W program (Thompson et al. 1994), inbuilt in the genetic analysis package MEGA version 4.0 (Tamura et al. 2007). Although mitochondrial amplification is known to be less complicated than that of nuclear genetic markers, matriarch samples were replicated independently at lease twice to ensure accurate genotyping. Offspring of known mother-calf relationships were sequenced only once but at both strands.

Accuracy of pedigree and relatedness values

Hypothesized and estimated relatedness values of 121 known mother-calf pairs (1st order relatives) and 81 known half sibs (2nd order relations) were well matched (Table S1). Similarly, these known pairs were used to assess the accuracy of pedigree assignments from ML Relate, which assigned 87% of known 1st and 2nd order relationships correctly. ML Relate does not distinguish 3rd order relationships from unrelated; 57% of known 3rd order relations were categorized as unrelated (Table S1).

Discussion

Group stability and matriarch age

Should hierarchical social organization emerge through the fission process of genetic groups, it would be plausible that fissions would be more common among less related groups (i.e. those groups for which the cohesive forces of relatedness were weakest). However, the greatest seasonal changes in group cohesion were found among families led by older matriarchs, not those groups least related. Two other obvious factors thought to influence the propensity of groups to fission, group size and calf ratio, also were not significant variables. The importance of matriarch age in group cohesion, in part, may be explained by the fact that older matriarchs tended to lead larger groups, which are likely to experience higher levels of intra-group competition during stressful periods. This enhanced competition potentially drives more frequent fission events or satellite affiliations—where females remain in relatively close proximity, < 1-2 km, potentially alleviating social stress while still accessing some benefits. The benefits of associating with older matriarchs driving larger group sizes are well recognized, including higher general social dominance rank and its repercussions (Wittemyer & Getz 2007; Wittemyer et al. 2007), higher survivorship during periods of stress apparently related to greater ecological and social knowledge (Foley et al. 2008), and higher general fitness (McComb et al. 2001). As such, the equilibrium point between the costs and benefits of group affiliation is likely to vary in relation to group characteristics like matriarch age, thus moderating the impact relatedness has on social cohesion.

Though speculative, this trend also may be impacted by the fact that some of the least related groups appear to contain “orphaned” females, who may maintain close affiliation with their adopted group in response to previous traumatic experience. Observational data over multiple years demonstrates that unrelated pairs of females within 2nd tier group have associative bonds as strong as many mother-calf pairs. Statistically, we could not discern the degree of relatedness among 2nd tier pairs based on association indices, as no significant difference in A.I. values was found between unrelated females, mother-calf and sibling pairs.

Impact of predation on social structure: Comparing Amboseli to Samburu

Methodological differences in analysis of the genetic basis for social behavior make direct comparison between results from Samburu and Amboseli difficult. For instance, association indices of dyads in Archie et al. 2006 core social groups varied between 0.2-1.0 (and A.I. among bond group dyads do not appear to differ substantially from this range), whereas 2nd tier “core” groups have A.I. > 0.65 by definition. Therefore, it appears dyads that were categorized as 3rd and 4th tier affiliates in Samburu could be considered “core” affiliates in Amboseli. Regardless, qualitative comparison clearly demonstrates stark differences between these populations. In Amboseli, the genetic basis for social affiliation across this range of A.I. values is unequivocal, with the only 2 exceptions (of 236 females analyzed) relating to single females immigrating into non-relative groups. Non-kin social group members were much more common in the Samburu population, including a lack of correlation between A.I. and relatedness values among 2nd tier pairs (Fig. 1 and Table 2).
Table S1

Known pedigree relationships (from field observations) are compared with microsatellite derived relatedness estimates (both Queller and Goodnight (1989) and Kalinowski et al. (2006) ML relate values). Expected r-values are listed under the known pedigree relationships. N is the number of known pairs analyzed. The last three shaded columns show ML relate pedigree assignments across corresponding categories, with the number (and percent of total in parentheses) from each known relationship category assigned to each pedigree category.

Known Relationship / N / Q&G
r-value / Std. Error / M.L.
r-value / Std. Error / Parent-Offspring/ Full Siblings / Half Siblings / Unrelated
Parent-Offspring
(r = 0.50) / 121 / 0.490 / 0.008 / 0.505 / 0.006 / 105 (87%) / 16 (13%) / 0
Half-Sibling
(r = 0.25) / 81 / 0.275 / 0.013 / 0.264 / 0.012 / 5 (6%) / 70 (87%) / 6 (7%)
Grandmother-GrandChild
(r = 0.25) / 9 / 0.226 / 0.023 / 0.231 / 0.033 / 0 / 8 (89%) / 1 (11%)
Aunt-Niece/Nephew
(r = 0.125) / 36 / 0.119 / 0.021 / 0.112 / 0.015 / 0 / 16 (44%) / 20 (56%)
1st Cousin
(r = 0.125) / 8 / 0.098 / 0.066 / 0.095 / 0.047 / 0 / 3 (37%) / 5 (63%)

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