Journal of Heredity 2004:95(1):19–28 ª 2004 The American Genetic Association DOI: 10.1093/jhered/esh006 Phylogenetic and Phylogeographic Analysis of Iberian Lynx Populations W. E. JOHNSON,J.A.GODOY,F.PALOMARES,M.DELIBES,M.FERNANDES,E.REVILLA, AND S. J. O’BRIEN From the Laboratory of Genomic Diversity, National Cancer Institute-FCRDC, Frederick, MD 21702-1201 (Johnson and O’Brien), Department of Applied Biology, Estacio´ n Biolo´ gica de Don˜ana, CSIC, Avda. Marı´a Luisa s/n, 41013, Sevilla, Spain (Godoy, Palomares, Delibes, and Revilla), and Instituto da Conservac¸a˜o da Natureza, Rua Filipe Folque, 46, 28, 1050-114 Lisboa, Portugal (Fernandes). E. Revilla is currently at the Department of Ecological Modeling, UFZ-Center for Environmental Research, PF 2, D-04301 Leipzig, Germany. The research was supported by DGICYT and DGES (projects PB90-1018, PB94-0480, and PB97-1163), Consejerı´a de Medio Ambiente de la Junta de Andalucı´a, Instituto Nacional para la Conservacion de la Naturaleza, and US-Spain Joint Commission for Scientific and Technological Cooperation. We thank A. E. Pires, A. Piriz, S. Cevario, V. David, M. Menotti-Raymond, E. Eizirik, J. Martenson, J. H. Kim, A. Garfinkel, J. Page, C. Ferris, and E. Carney for advice and support in the laboratory and J. Calzada, J. M. Fedriani, P. Ferreras, and J. C. Rivilla for assistance in the capture of lynx. Museo Nacional de Ciencias Naturales, Don˜ana Biological Station scientific collection, Don˜ana National Park, and Instituto da Conservac¸a˜o da Natureza of Portugal provided samples of museum specimens. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. government. Address correspondence to W. E. Johnson at the address above. Abstract The Iberian lynx (Lynx pardinus), one of the world’s most endangered cat species, is vulnerable due to habitat loss, increased fragmentation of populations, and precipitous demographic reductions. An understanding of Iberian lynx evolutionary history is necessary to develop rational management plans for the species. Our objectives were to assess Iberian lynx genetic diversity at three evolutionary timescales. First we analyzed mitochondrial DNA (mtDNA) sequence variation to position the Iberian lynx relative to other species of the genus Lynx. We then assessed the pattern of mtDNA variation of isolated populations across the Iberian Peninsula. Finally we estimated levels of gene flow between two of the most important remaining lynx populations (Don˜ana National Park and the Sierra Morena Mountains) and characterized the extent of microsatellite locus variation in these populations. Phylogenetic analyses of 1613 bp of mtDNA sequence variation supports the hypothesis that the Iberian lynx, Eurasian lynx, and Canadian lynx diverged within a short time period around 1.53–1.68 million years ago, and that the Iberian lynx and Eurasian lynx are sister taxa. Relative to most other felid species, genetic variation in mtDNA genes and nuclear microsatellites were reduced in Iberian lynx, suggesting that they experienced a fairly severe demographic bottleneck. In addition, the effects of more recent reductions in gene flow and population size are being manifested in local patterns of molecular genetic variation. These data, combined with recent studies modeling the viability of Iberian lynx populations, should provide greater urgency for the development and implementation of rational in situ and ex situ conservation plans. The Iberian lynx (Lynx pardinus), the largest remaining cat teristics and are distinguished primarily by their relative species in southwestern Europe, is one of the world’s sizes (Nowell and Jackson 1996) and a few cranial or most endangered felids (Nowell and Jackson 1996). The postcranial skeletal measurements (Garcia-Perea 1992). genus Lynx, including the Iberian lynx, bobcat (L. rufus), There has been consistent support for a monophyletic Canadian lynx (L. canadensis), and Eurasian lynx (L. lynx) ancestry for the four species from morphological (Nowak descend from a common ancestor that diverged from 1999) and DNA-based analyses ( Janczewski et al. 1995; other cat species more than 6 million years ago ( Johnson Johnson et al. 1996; Johnson and O’Brien 1997; Pecon- and O’Brien 1997). These four Lynx species have almost Slattery and O’Brien 1998). However, the hierarchical completely disjunctive distributions and occupy different relationships among lynx species and their recognition as habitats. However, they share numerous physical charac- unique species have been debated. 19 Journal of Heredity 2004:95(1) Fossil records suggest that lynx species originated in the west (Rodriguez and Delibes 1992). The nearest lynx North America (MacFadden and Galiano 1981; Martin populations are found in the Sierra Morena Mountains 1989). The bobcat appears to represent the earliest lineage to (Figure 1), where several of the largest remaining lynx diverge (Johnson and O’Brien 1997), but subsequent metapopulations are suspected to still exist. This mountain evolutionary history is less clear. The Iberian lynx and range, perhaps one of the keys to the future preservation of Eurasian lynx may be derived from an ancestral lynx species the Iberian lynx, has received increasing attention by (Lynx issiodorensis) whose remains have been found in China conservationist and resource managers. (Wederlin 1981). The Canadian and Eurasian lynx have been The objectives of this study were to quantify the hypothesized to be sister taxa (Wederlin 1981). The Iberian evolutionary relationship of the Iberian lynx with the other lynx and Eurasian lynx were both found in central Europe Lynx species using mtDNA sequence variation, describe during the Pleistocene (Kurten 1968; Kurten and Grandqvist patterns of lynx mtDNA variation across the Iberian 1987), but may never have had significantly overlapping peninsula, and compare patterns of microsatellite size geographic ranges. variation and estimate gene flow between the important The distribution and population sizes of the Eurasian and lynx populations of Don˜ana and Sierra Morena. An Iberian lynx have been reduced significantly during the last improved understanding of patterns of Iberian lynx two centuries. The Eurasian lynx was extirpated from most molecular genetic variation and recent evolutionary history of central and southern Europe during the 19th century is necessary to develop rational management plans for the (Breitenmoser and Breitenmoser-Wursten 1990). Similarly, species (Vargas 2000) and provide further insights into the by the beginning of the 20th century the Iberian lynx was rare biogeographical history of the Iberian peninsula. in northern Spain and by the 1960s its range was essentially limited to isolated populations in the southwestern portion of the peninsula (Rodriguez and Delibes 1990). By the 1990s, Methods it was estimated that no more than 1000 lynx were restricted DNA Extraction to fewer than 50 disjunct breeding areas that could be grouped into less than 10 distinct subpopulations (Castro Lynx DNA was extracted from blood and tissue samples and Palma 1996; Rodriguez and Delibes 1992). Only two of from 20 wild animals captured or found dead during these subpopulations, Sierra Morena and Montes de Toledo capturing and radio-tracking of lynx from 1985 to 2000, (Figure 1) inhabit areas larger than 2000 km2, which is of and from 35 tissue and skin samples in scientific collections major concern since between 1960 and 1988 Iberian lynx are from seven metapopulations throughout the range of the presumed to have disappeared from most of the remaining Iberian lynx (Table 1). Blood samples were stored in four small habitat patches (from 91% of the areas smaller than volumes of lysis buffer (0.1 M Tris-HCl pH 8.0; 0.1 M Na- 1000 km2). This corresponds to an 80% reduction in EDTA; 0.01 M NaCl, 0.5% SDS) and tissue samples were occupied range (Rodriguez and Delibes 1990). However, kept frozen or at room temperature in a dimethyl sulfoxide current geographical limits and population sizes are not well (DMSO)-salt solution (20% DMSO, 0.25M Na-EDTA, and known and continued loss of habitat and the disappearance NaCl to saturation, pH 8.0). From museums specimens, of lynx from previously occupied areas suggests that fewer approximately 1 cm2 of skin was cut with a sterile scalpel than 500 individuals may now remain (Beltra´n and Delibes after superficial cleaning with 10% commercial bleach, 1994; Palomares et al. 2000; Pires and Fernandes 2003). distilled water, and 70% ethanol. DNA extractions of The best known of the Iberian lynx populations inhabits museum materials were conducted in a dedicated room Don˜ana National Park, Andalusia, where field data on the along with extraction blanks to monitor for contamination. species have been collected since the 1950s and radio- DNA was extracted following standard proteinase K/phenol tracking studies have been conducted for more than 15 years chloroform protocols (Sambrook et al. 1989); for museum (e.g., Ferreras et al. 1997; Gaona et al. 1998; Palomares et al. skin extractions, several prewashes with NTE pH 9.0 (NaCl 1991, 2001). The Don˜ana metapopulation (1500 km2)of 10 mM; Tris base 50 mM; EDTA 20 mM) were included to approximately 40–50 individuals currently is distributed in at remove possible enzyme inhibitors. For comparative least four distinct areas that were last completely connected purposes we used DNA extracted using similar techniques during the middle of the last century. Within the Don˜ana in previous studies from three European lynx (Lly 12, 15, and metapopulation, the population occupying the protected 16), two Canadian lynx (Lca 3 and 7), five bobcat (Lru 6, 26, parkland areas is relatively stable, while mortality in the less- 48, 68, and 73), two marbled cats (Pardofelis marmorata) (Pma 4 protected areas is higher, especially among dispersing and 5), and one clouded leopard (Neofelis nebulosa) (Nne 80) animals (70–85% mortality rate) (Ferreras et al.