Journal of Systematics and Evolution 00 (0): 1–11 (2012) doi: 10.1111/j.1759-6831.2012.00206.x Research Article North-south population subdivision of Juniperus seravschanica in Kyrgyzstan revealed through novel plastid DNA markers Ormon SULTANGAZIEV § Heino KONRAD § Silvio SCHUELER Thomas GEBUREK ∗ (Department of Genetics, Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Hauptstrasse 7, A-1140 Vienna, Austria) Abstract Junipers are main components of semiarid forests in Central Asia. Conservation of these plant genetic resources should be based on an understanding of factors that have shaped species-level genetic variation. We used Juniperus seravschanica Kom. as a model species to investigate patterns and processes that may be associated with these factors. Novel plastid DNA markers (two minisatellites, one transversion, one indel) were identified and applied to investigate haplotype diversity and population structure in Kyrgyzstan. In total, 540 individuals from 15 populations were analyzed and 11 haplotypes detected. Strong divergence between populations from northern and southern Kyrgyzstan was evident from the haplotype distribution. Gene diversity within populations ranged from 0.083 to 0.765, and was on average higher in southern (0.687) than in northern populations (0.540). A similar pattern was detected in allelic richness. Analysis of molecular variance (AMOVA) revealed that 11.9% of the total genetic variation was due to differences among regions, 1.5% among populations, and 86.6% within populations. N ST was not significantly different from G ST (0.125), suggesting no evidence of a phylogeographic pattern. A Mantel test detected a weak but significant isolation-by-distance pattern for the whole dataset and southern populations separately. These results suggest that the north of Kyrgyzstan was relatively recently colonized by migrants from southern populations, probably associated with favorable conditions during the early Holocene. The humid Fergana Valley and Fergana Range are probable ecological barriers to gene flow between northern and southern populations. Key words Central Asia, conservation, minisatellite, phylogeography, population history, semi-arid forest. Diverse modes of species movement and drastic changes in population structure of forest tree species have been detected following glaciation, which is im- portant for understanding the processes that may have shaped current genetic patterns, and for developing management strategies to conserve them more effec- tively (Frankham et al., 2002). The population history of many tree species in Europe and North America is relatively well understood (e.g., Petit et al., 2003; Soltis et al., 2006), but very little is known about other re- gions of the temperate north, including Central Asia. Although relatively few details are known on the vege- tation history of the latter area, various lines of evidence indicate that very cold (permafrost) and arid conditions prevailed in this region during the last glacial maxi- mum (LGM; ca. 18 000 years BP) and early Holocene (Aubekerov & Gorbunov, 1999), which drove the forest to refugia that were further south. After these desert-like Received: 17 November 2011 Accepted: 11 May 2012 § These authors contributed equally to this work. ∗ Author for correspondence. E-mail: thomas.geburek@bfw.gv.at. Tel.: +43- 1-87838-2109. Fax: +43-1-87838-2250. conditions, a warmer and more humid period (8000– 5000 years BP) followed in which there was more ex- tensive vegetation cover. Later the climate became drier but more stable (Adams & Faure, 1997). Here, we ana- lyze the genetic diversity and population differentiation of a forest tree species, Juniperus seravschanica Kom. (=J. polycarpos var. seravschanica [Kom.] Kitam.), in Kyrgyzstan to improve our understanding of the overall vegetational history of this region. Kyrgyzstan is a mountainous country that is lo- cated in the western (outer) part of the Tien-Shan range. The climate is mainly semi-arid and only 4.2% of the land surface is covered by continuous forests (Musuraliev, 2004). These are predominately juniper (Juniperus L., Cupressaceae) forests (locally called “ar- cha”) that are found typically on dry foothills or at mid to high altitudes, between 1000 and 3500 m above sea level (asl), where trees take on a prostrate growth form. Natural juniper forests in Kyrgyzstan occur in two parts of the country: the southwest and the north- west, with the humid Fergana Valley and the Fergana Range dividing the distribution. The most important contribution to the understanding of the vegetation his- tory of western Kyrgyzstan was provided by Beer et al. C  2012 Institute of Botany, Chinese Academy of Sciences