TEST OF INTERACTION IN THE ANALYSIS OF MOLECULAR VARIANCE

The genomic diversity, expressed in the differences between molecular haplotypes of a group of individuals, can be divided into components of variability between and within some factor of classification of the individuals. For such variance partitioning, molecular analysis of variance (AMOVA) is used, which is constructed from the multivariate distances between pairs of haplotypes. The classical AMOVA allows the evaluation of the statistical significance of two or more hierarchical factors and consequently there is no interaction test between factors. However, there are situations where the factors that classify individuals are crossed rather than nested, that is, all the levels of a factor are represented in each level of the other one. This paper proposes a statistical test to evaluate the interaction between crossed factors in a Non-Hierarchical AMOVA. The null hypothesis of interaction establishes that the molecular differences between individuals of different levels of a factor are the same for all the levels of the other factor that classifies them. The proposed analysis of interaction in a Non-Hierarchical AMOVA includes: calculation of the distance matrix and partition of it into blocks, subsequent calculation of residuals and analysis of non-parametric variance on the residuals. Its implementation is illustrated in simulated and real scenarios. The results suggest that the proposed interaction test for the Non-Hierarchical AMOVA presents high power. Key words: genetic variability, non-parametric methods, distances matrix, AMOVA.

Post-glacial recolonization of insular Newfoundland across the Strait of Belle Isle gave rise to an endemic subspecies of woodland caribou, Rangifer tarandus terranovae (Bangs, 1896): evidence from mtDNA haplotypes

Post-glacial origins of woodland caribou (Rangifer tarandus subsp.) on the island of Newfoundland and their relationship to mainland populations have been uncertain. Sequence analysis of 2223 bp of the mitochondrial DNA control region and cytochrome b gene from 233 Newfoundland caribou identified 32 haplotypes in four major clades. Comparison with other Nearctic caribou confirms a closer affinity of the basal Clade A with animals from the mainland, and as an outgroup to Clades B, C, and D that are endemic to the island. This indicates re-entry of caribou to post-glacial Newfoundland across the Strait of Belle Isle from Labrador, rather than from southern coastal refugia. Newfoundland caribou are a distinct subspecies, Rangifer tarandus terranovae (Bangs, 1896). Hierarchical AMOVA shows significant clinal differentiation of the major clades from northwest to southeast across the island. The isolated Avalon Peninsula population in the extreme southeast is genetically depauperate. Founder effects are evident in herds introduced to previously unoccupied areas by wildlife managers over the past 40–50 years. Reindeer introduced in the early 20th century have not contributed to mtDNA diversity in Newfoundland caribou.

GENETIC VARIATION OF Tor tambroides (Bleeker, 1854) ALONG BATANG TARUSAN RIVER, WEST SUMATERA: IMPLICATIONS FOR STOCK IDENTIFICATION

Mahseer (<em>Tor tambroides</em>, Bleeker, 1854) is an important consumption fish species in the Batang Tarusan River, located in the West Sumatera, Indonesia. In this study the CO1 of mtDNA sequence data were used to investigate genetic variability within and between populations of mahseer. Twenty four tissue samples were collected for genetic analysis in the Batang Tarusan River. Genetic analysis revealed two different haplotypes were existed. The overall nucleotide and haplotype variability were low in all sampling sites. Hierarchical AMOVA analysis showed that mahseer populations form a single panmictic population with low FST= 0.02794; p = 0.418 and high gene flow among population sampling. Corroborated result by genetic analysis; there is a strong argument suggesting that the populations could be treated as a single stock unit.

Low level of genetic variation within Melica transsilvanica populations from the Kraków-Częstochowa Upland and the Pieniny Mts revealed by AFLPs analysis

Fragmented distribution, the breeding system and effects of genetic drift in small-size populations occurring at edge of the species range play an important role in shaping genetic diversity of such a species. <em>Melica transsilvanica</em> is a plant rare in the flora of Poland, where it reaches the northern limit of its continuous range. Amplified Fragment Length Polymorphism (AFLP) DNA profiling method was applied to measure genetic diversity among and within populations of <em>M. transsilvanica</em>. Additionally, genetic relationships between M. transsilvanica and Melica ciliata, two closely related species, were explored. A total of 68 plants from 7 populations of <em>M. transsilvanica</em> and 24 plants from 2 populations of <em>M. ciliata</em>, collected in Poland and outside it, were analyzed. Using 294 AFLP fragments from 3 primer combinations, accessions were grouped into two major clusters associating with <em>M. ciliata</em> and <em>M. transsilvanica</em>, respectively. Further, two subclusters, corresponding to the samples collected from the Pieniny Mts and from the Kraków - Częstochowa Upland were clearly distinguished within the <em>M. transsilvanica</em> group. The hierarchical AMOVA exhibited significant genetic distinction between these geographic regions (60.89%, p &lt; 0.001). The obtained results showed that the most genetic diversity resided between the populations of <em>M. transsilvanica</em> (86.03%) while considerably lower genetic variation was found within the populations (13.97%), which is consistent with the results reported for self-plants. The low level of AFLP genetic variation of <em>M. transsilvanica</em> can be caused by the geographic isolation of populations, which preserves the dominant self-mating breeding system of the species. Individual populations of <em>M. transsilvanica</em> are characterized by isolated gene pools differing by a small number of loci.

Mitochondrial DNA diversity and population structure of a forest-dependent rodent, Praomys taitae (Rodentia: Muridae) Heller 1911, in the fragmented forest patches of Taita Hills, Kenya

The population genetic structure of the forest-dependent rodent, Praomys taitae, sampled from nine indigenous forest fragments distributed over three ranges of the Taita Hills in Kenya, was determined using mitochondrial DNA (mtDNA) control region sequence variation. Thirty-three unique haplotypes were observed in a total sample of 132 individuals, whereas the number of different haplotypes per population ranged from two to 10. An overall low nucleotide diversity of 0.9% was observed in the total sample but varied widely between populations (0.2–1.3%). Significant genetic differentiation was observed in 30 of the 36 possible pair-wise comparisons between populations, while a hierarchical AMOVA revealed significant genetic subdivision between groups of populations on the three hill ranges of Dabida, Mbololo and Kyulu (FCT = 0.404, P less than 0.01), among populations on each of the hill ranges (FSC = 0.112, P less than 0.01) and among populations in the total sample (FST = 0.471, P less than 0.001). Demographic history analyses based on pair-wise nucleotide sequence mismatch distributions revealed that all the populations were in mutation-drift disequilibrium except the populations of the Kyulu and Ronge forest fragments.