Population structure and dispersal in a patchy landscape: nuclear and mitochondrial markers reveal area effects in the spider Theridion californicum (Araneae: Theridiidae) PETER J. P. CROUCHER 1 *, GEOFF S. OXFORD 2 and ROSEMARY G. GILLESPIE 1 1 Department of Environmental Science, Policy and Management, Division of Insect Biology, University of California, Berkeley, CA 94720, USA 2 Department of Biology (Area 14), University of York, Heslington, York, YO105DD, UK Received 24 March 2011; revised 29 May 2011; accepted for publication 30 May 2011 Changes in land use have a major effect on patterns of biodiversity. However, few studies have examined the demographic and genetic shifts associated with a return to semi-natural habitat following extended periods of human disturbance. Here we examine patterns of population structure in a spider restricted to the Pacific coastal strip of North America that exhibits an exuberant colour polymorphism. We use mitochondrial DNA and AFLP markers to examine genetic structure and estimate gene flow. The results show contrasting, gender-specific patterns between these markers that suggest limited dispersal, combined with area effects most likely caused by expansion from refugial habitat patches following land-management changes in a region of the San Francisco East Bay. Colour-morph frequencies are not correlated with this complex genetic structure. Thus, unlike the classical area effects that were based on colour morphs, we demonstrate in T. californicum signals of historical contingency at neutral loci but not at the Colour locus, where traces of past events have been obliterated by balancing selection. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 600–620. ADDITIONAL KEYWORDS: balancing selection – colour polymorphism – dispersal – disturbance – gene-flow – land-use change – range expansion. INTRODUCTION Landscape dynamics have played a key role in shaping biodiversity in the historical and recent past (Chiucchi & Gibbs, 2010). The current rapid rate and extent of habitat modification in particular has led to diverse effects on species, ranging from fragmenta- tion and extinction (e.g. Mayer, Schiegg & Pasinelli, 2009), to hybridization (e.g. Dodd & Kashani, 2003), population expansion (Bloor, Kemp & Brown, 2008) and invasion of new habitats (Ewers & Didham, 2006). As a means to understand the processes under- lying these patterns, numerous studies have applied phylogeographic methods based on molecular data, providing key insights into how populations have responded, and will continue to respond, to habitat modification. Most of these studies have focused on situations in which the habitat has been modified from a ‘natural’ state (e.g. Vandergast et al., 2007). Very few have examined phylogeographic shifts asso- ciated with the return of habitat to a natural state following extended periods of disturbance (notable exceptions include Chatzimanolis & Caterino, 2009). Here, we explore a situation where the landscape has undergone historical fragmentation and recent recovery and examine how a species with potentially limited dispersal has responded to such modifications. The coastal region of western North America, in particular around the East Bay of San Francisco, is known for its high levels of endemism at the subspe- cies level (Davis et al., 2008). For example, the sala- mander Batrachoseps attenuatus (Plethodontidae) shows high levels of genetic diversity and deep diver- gences within the region (Martínez-Solano, Jockusch *Corresponding author. E-mail: croucher@berkeley.edu Biological Journal of the Linnean Society, 2011, 104, 600–620. With 6 figures © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 600–620 600 Downloaded from https://academic.oup.com/biolinnean/article-abstract/104/3/600/2452391 by guest on 15 June 2020