Ceanothus: Taxonomic patterns in life history responses to fire.

PREMISE: Ceanothus (Rhamnaceae) is a large genus of shrubs that dominate California chaparral and are resilient to fires. Persistence is ensured by resprouting and/or seedling recruitment from dormant seed banks. Some species do both and others, the obligate seeders, are entirely dependent on seedling recruitment. The distribution of these two modes within the genus is poorly documented. METHODS: We used all available publications that document species responses to fire and filled most gaps in the literature based on extensive field studies of more than 60 recent wildfires in California. RESULTS: The genus is divided into two subgenera, Ceanothus and Cerastes. Ceanothus is widely considered to comprise mostly resprouting species and Cerastes to consist of only obligate seeders. The subgenus Ceanothus includes resprouting species throughout their range from the eastern United States and Midwest to western United States. Within the California Floristic Province (CFP), a few species are unique in producing massive lignotubers that develop from repeated fires; however, within the CFP, the majority of species in this subgenus do not resprout and are obligate seeders. Two have disjunct subspecies that are facultative seeders or obligate seeders. CONCLUSIONS: Previously, speciation in this genus was contended to have occurred in the late Miocene within the CFP. The syndrome of obligate seeding is most strongly represented in this region, and we hypothesize that evolution of this syndrome was a response to increased predictability of fire driven by the Mediterranean climate and the long interval between fires.

Sensitive Hydraulic and Stomatal Decline in Extreme Drought Tolerant Species of California Ceanothus.

Identifying the physiological mechanisms by which plants are adapted to drought is critical to predict species responses to climate change. We measured the responses of leaf hydraulic and stomatal conductances (Kleaf and gs, respectively) to dehydration, and their association with anatomy, in seven species of California Ceanothus grown in a common garden, including some of the most drought-tolerant species in the semi-arid flora. We tested for matching of maximum hydraulic supply and demand and quantified the role of decline of Kleaf in driving stomatal closure. Across Ceanothus species, maximum Kleaf and gs were negatively correlated, and both Kleaf and gs showed steep declines with decreasing leaf water potential (i.e., a high sensitivity to dehydration). The leaf water potential at 50% decline in gs was linked with a low ratio of maximum hydraulic supply to demand (i.e., maximum Kleaf:gs). This sensitivity of gs, combined with low minimum epidermal conductance and water storage, could contribute to prolonged leaf survival under drought. The specialized anatomy of subg. Cerastes includes trichomous stomatal crypts and pronounced hypodermis, and was associated with higher water use efficiency and water storage. Combining our data with comparative literature of other California species, species of subg. Cerastes show traits associated with greater drought tolerance and reliance on leaf water storage relative to other California species. In addition to drought resistance mechanisms such as mechanical protection and resistance to embolism, drought avoidance mechanisms such as sensitive stomatal closure could contribute importantly to drought tolerance in dry-climate adapted species.

Phylogenomic perspectives on speciation and reproductive isolation in a North American biodiversity hotspot: an example using California sages (Salvia subgenus Audibertia: Lamiaceae).

BACKGROUND AND AIMS: The California Floristic Province (CA-FP) is the most species-rich region of North America north of Mexico. One of several proposed hypotheses explaining the exceptional diversity of the region is that the CA-FP harbours myriad recently diverged lineages with nascent reproductive barriers. Salvia subgenus Audibertia is a conspicuous element of the CA-FP, with multiple sympatric and compatible species. METHODS: Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyse contemporaneous patterns of gene flow and mechanical reproductive isolation. KEY RESULTS: Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades, indicating that reproductive barriers arise with increasing genetic divergence. Species are generally not mechanically isolated, suggesting that it is unlikely to be the primary factor leading to reproductive isolation. CONCLUSIONS: Rapid, recent speciation with some interspecific gene flow in conjunction with the onset of a Mediterranean-like climate is the underlying cause of extant diversity in Salvia subgenus Audibertia. Speciation has largely not been facilitated by gene flow. Its signal in the nuclear genome seems to mostly be erased by backcrossing, but organellar genomes each capture different instances of historical gene flow, probably characteristic of many CA-FP lineages. Mechanical reproductive isolation appears to be only part of a mosaic of factors limiting gene flow.

Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae).

We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades-inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)-began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.

Phylogeography and cohesion species delimitation of California endemic trapdoor spiders within the Aptostichus icenoglei sibling species complex (Araneae: Mygalomorphae: Euctenizidae).

Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population-level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genus Aptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, the Aptostichus icenoglei complex, which comprises the three sibling species, A. barackobamai, A. isabella, and A. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species-based approach. We used genomic-scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries within A. icenoglei.

Genomic data reveal local endemism in Southern California Rubber Boas (Serpentes: Boidae, Charina) and the critical need for enhanced conservation actions.

The mountains of southern California represent unique, isolated ecosystems that support distinct high-elevation habitats found nowhere else in the area. Analyses of several moisture-dependent species across these sky-islands indicate they exist as locally endemic lineages that occur across these fragmented mountains ranges. The Rubber Boa is a semi-fossorial snake species that is widely distributed in the cooler and more moist ecoregions regions of western North America, including isolated populations across southern California mountain ranges. We developed a genomic and ecological dataset to examine genetic diversity within Rubber Boas and to determine if the endemic Southern Rubber Boa represents a distinct lineage. We quantified current and future habitat suitability under a range of climate change scenarios, and discuss the possible environmental threats facing these unique montane isolates. Our results support four major lineages within Rubber Boas, with genetic breaks that are consistent with biogeographic boundaries observed in other co-distributed, cool-temperature, moisture adapted species. Our data support previous studies that the Southern Rubber Boa is an independent evolutionary unit and now includes multiple locally endemic sky-island populations, restricted to isolated mountain tops and ranges across southern California. Analyses of future habitat suitability indicate that many of these sky-island populations will lose most of their suitable habitat over the next 70 years given predicted increases in drought, rising temperatures, and wildfires. Collectively these data emphasize the critical conservation needs of these montane ecosystems in southern California under current and projected climate change conditions.

Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca).

Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.

Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project.

The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California's marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.

Phylogeography of an endemic California silkmoth genus suggests the importance of an unheralded central California province in generating regional endemic biodiversity.

The California Floristic province is a biodiversity hotspot. Understanding the phylogeographic patterns that exist in this diverse region is essential to understanding its evolution and for guiding conservation efforts. Calosaturnia is a charismatic silkmoth genus endemic to large portions of the region with three described species, C. mendocino, C. walterorum, and C. albofasciata. We sampled all three species from across their ranges, sequenced 1463 bp of mitochondrial COI and 1941 bp of nuclear DNA from three genes, and reconstructed phylogenetic relationships and estimated divergence times within the lineages. All three species show pronounced evidence of isolation and, in two cases, secondary reconnection. An unexpected monophyletic mtDNA lineage was found in the Central Coast region, in a region thought to represent an intergrade between C. mendocino and C. walterorum. Our genetic data also significantly revise previous hypotheses as to which species occur in which regions, suggesting that historical ecological changes around four Ma ago isolated some lineages, and a secondary isolation event two Ma ago led to isolation of populations both in the Central Coast region and the southern Sierra Nevada. Our results add to a currently under-appreciated pattern suggesting that coastal Central California is not a transition zone between Northern and Southern California Floristic Province faunas but rather its own unique, periodically isolated, biogeographic region. They also suggest cryptic diversity may be present in many other currently unrecognized groups. Additional research should focus on this central California region because many species may be highly restricted in range and in need of conservation attention.

A revision of the shield-back katydid genus Neduba (Orthoptera: Tettigoniidae: Tettigoniinae: Nedubini).

The Nearctic shield-back katydid genus Neduba is revised. Species boundaries were demarcated by molecular phylogenetic analysis, morphology, quantitative analysis of calling songs, and karyotypes. Nine previously described species are redescribed: N. carinata, N. castanea, N. convexa, N. diabolica, N. extincta, N. macneilli, N. propsti, N. sierranus, and N. steindachneri, and twelve new species are described: N. ambagiosa sp. n., N. arborea sp. n., N. cascadia sp. n., N. duplocantans sp. n., N. inversa sp. n., N. longiplutea sp. n., N. lucubrata sp. n., N. oblongata sp. n., N. prorocantans sp. n., N. radicata sp. n., N. radocantans sp. n., and N. sequoia sp. n. We chose a lectotype for N. steindachneri and transferred N. picturata from a junior synonym of N. diabolica to a junior synonym of N. steindachneri. Diversification in this relict group reflects cycles of allopatric isolation and secondary contact amidst the tumultuous, evolving geography of western North America. The taxonomy and phylogenies presented in this revision lay the groundwork for studies of speciation, biogeography, hybrid zones, and behavioral evolution. Given that one Neduba species is already extinct from human environmental disturbance, we suggest conservation priorities for the genus.

Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex.

BACKGROUND: Mygalomorph spiders represent a diverse, yet understudied lineage for which genomic level data has only recently become accessible through high-throughput genomic and transcriptomic sequencing methods. The Aptostichus atomarius species complex (family Euctenizidae) includes two coastal dune endemic members, each with inland sister species - affording exploration of dune adaptation associated patterns at the transcriptomic level. We apply an RNAseq approach to examine gene family conservation across the species complex and test for patterns of positive selection along branches leading to dune endemic species. RESULTS: An average of ~ 44,000 contigs were assembled for eight spiders representing dune (n = 2), inland (n = 4), and atomarius species complex outgroup taxa (n = 2). Transcriptomes were estimated to be 64% complete on average with 77 spider reference orthologs missing from all taxa. Over 18,000 orthologous gene clusters were identified within the atomarius complex members, > 5000 were detected in all species, and ~ 4700 were shared between species complex members and outgroup Aptostichus species. Gene family analysis with the FUSTr pipeline identified 47 gene families appearing to be under selection in the atomarius ingroup; four of the five top clusters include sequences strongly resembling other arthropod venom peptides. The COATS pipeline identified six gene clusters under positive selection on branches leading to dune species, three of which reflected the preferred species tree. Genes under selection were identified as Cytochrome P450 2c15 (also recovered in the FUSTr analysis), Niemann 2 Pick C1-like, and Kainate 2 isoform X1. CONCLUSIONS: We have generated eight draft transcriptomes for a closely related and ecologically diverse group of trapdoor spiders, identifying venom gene families potentially under selection across the Aptostichus atomarius complex and chemosensory-associated gene families under selection in dune endemic lineages.

Proposal of 'Candidatus Frankia californiensis', the uncultured symbiont in nitrogen-fixing root nodules of a phylogenetically broad group of hosts endemic to western North America.

The genus Frankia comprises a group of nitrogen-fixing actinobacteria that form root-nodule symbioses with perennial dicotyledonous plants in the nitrogen-fixing clade. These bacteria have been characterized phylogenetically and grouped into four clusters (clusters 1-4). Cluster 2 contains mostly uncultured strains that induce nodules on species of the genera Datisca (Datiscaceae), Coriaria (Coriariaceae), Ceanothus (Rhamnaceae) and several genera in the family Rosaceae (Cercocarpus, Chamaebatia, Dryas, Purshia), all of which except members of the genus Coriaria are present within the California Floristic Province (CFP) or neighbouring areas of western North America. Those strains occurring in western North America are genetically very closely related to one another, and genetically distinct from strains characterized from other locales. We hereby propose to create a 'Candidatus Frankia californiensis' species for those cluster 2 strains of the genus Frankia with both high genetic similarity and a geographical distribution in or near the CFP.

A new species of Illacme Cook & Loomis, 1928 from Sequoia National Park, California, with a world catalog of the Siphonorhinidae (Diplopoda, Siphonophorida).

Members of the family Siphonorhinidae Cook, 1895 are thread-like eyeless millipedes that possess an astounding number of legs, including one individual with 750. Due to their cryptic lifestyle, rarity in natural history collections, and sporadic study over the last century, the family has an unclear phylogenetic placement, and intrafamilial relationships remain unknown. Here we report the discovery of a second species of Illacme, a millipede genus notable for possessing the greatest number of legs of any known animal on the planet. Illacme tobinisp. n. is described from a single male collected in a cave in Sequoia National Park, California, USA. After 90 years since the description of Illacme, the species represents a second of the genus in California. Siphonorhinidae now includes Illacme Cook & Loomis, 1928 (two species, USA), Kleruchus Attems, 1938 (one species, Vietnam), Nematozonium Verhoeff, 1939 (one species, South Africa) and Siphonorhinus Pocock, 1894 (eight species, India, Indonesia, Madagascar, Vietnam).

Tests of species-specific models reveal the importance of drought in postglacial range shifts of a Mediterranean-climate tree: insights from integrative distributional, demographic and coalescent modelling and ABC model selection.

Past climate change has caused shifts in species distributions and undoubtedly impacted patterns of genetic variation, but the biological processes mediating responses to climate change, and their genetic signatures, are often poorly understood. We test six species-specific biologically informed hypotheses about such processes in canyon live oak (Quercus chrysolepis) from the California Floristic Province. These hypotheses encompass the potential roles of climatic niche, niche multidimensionality, physiological trade-offs in functional traits, and local-scale factors (microsites and local adaptation within ecoregions) in structuring genetic variation. Specifically, we use ecological niche models (ENMs) to construct temporally dynamic landscapes where the processes invoked by each hypothesis are reflected by differences in local habitat suitabilities. These landscapes are used to simulate expected patterns of genetic variation under each model and evaluate the fit of empirical data from 13 microsatellite loci genotyped in 226 individuals from across the species range. Using approximate Bayesian computation (ABC), we obtain very strong support for two statistically indistinguishable models: a trade-off model in which growth rate and drought tolerance drive habitat suitability and genetic structure, and a model based on the climatic niche estimated from a generic ENM, in which the variables found to make the most important contribution to the ENM have strong conceptual links to drought stress. The two most probable models for explaining the patterns of genetic variation thus share a common component, highlighting the potential importance of seasonal drought in driving historical range shifts in a temperate tree from a Mediterranean climate where summer drought is common.

Evolutionary lessons from California plant phylogeography.

Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures-both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change.

Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province.

The California Floristic Province (CFP) in western North America is a globally significant biodiversity hotspot. Elucidating patterns of endemism and the historical drivers of this diversity has been an important challenge of comparative phylogeography for over two decades. We generated phylogenomic data using ddRADseq to examine genetic structure in Uroctonus forest scorpions, an ecologically restricted and dispersal-limited organism widely distributed across the CFP north to the Columbia River. We coupled our genetic data with species distribution models (SDMs) to determine climatically suitable areas for Uroctonus both now and during the Last Glacial Maximum. Based on our analyses, Uroctonus is composed of two major genetic groups that likely diverged over 2 million years ago. Each of these groups itself contains numerous genetic groups that reveal a pattern of vicariance and microendemism across the CFP. Migration rates among these populations are low. SDMs suggest forest scorpion habitat has remained relatively stable over the last 21 000 years, consistent with the genetic data. Our results suggest tectonic plate rafting, mountain uplift, river drainage formation and climate-induced habitat fragmentation have all likely played a role in the diversification of Uroctonus. The intricate pattern of genetic fragmentation revealed across a temporal continuum highlights the potential of low-dispersing species to shed light on small-scale patterns of biodiversity and the underlying processes that have generated this diversity in biodiversity hotspots.

Pleistocene radiation of the serpentine-adapted genus Hesperolinon and other divergence times in Linaceae (Malpighiales).

PREMISE OF THE STUDY: Hesperolinon (western flax; Linaceae) is endemic to the western United States, where it is notable for its high and geographically concentrated species diversity on serpentine-derived soils and for its use as a model system in disease ecology. We used a phylogenetic framework to test a long-standing hypothesis that Hesperolinon is a neoendemic radiation. METHODS: Five plastid and two ribosomal nuclear DNA gene regions were sampled from 105 populations of Hesperolinon, including all 13 recently recognized species across their known ranges. We used these data to generate population-level phylogenies of Hesperolinon. We also generated a robustly sampled chronogram of Linaceae using an eight-gene, 100-taxon supermatrix calibrated using fossil Linum pollen and a published chronogram of Malpighiales. KEY RESULTS: Most diversification in Hesperolinon has taken place in the past 1-2 million yr, much more recently than previous estimates. Only the earliest-diverging species, H. drymarioides, was resolved as a clade. Denser taxon and gene sampling generally support previously proposed relationships within Linaceae, but with more recent diversification of key clades. CONCLUSIONS: Hesperolinon is an excellent example of edaphic neoendemism, in support of Raven and Axelrod's hypothesis for the genus. Dense population-level sampling reveals a complex of incipient species, with clades poorly aligned with traditional morphological circumscriptions, likely due in part to continued gene flow. The diversification of Linaceae is more recent than previously estimated, and other recent radiations (e.g., Hugonia) warrant further study.

The sequoia-loving sprite, a new genus and species of fungus gnat (Diptera, Mycetophilidae) from California.

California is one of the most biologically diverse regions of the world, yet the diversity of fungus gnats (Mycetophilidae) remains largely undocumented within the state. A modest survey of these flies has led to the discovery of a new genus and species of gnat that lives alongside one of the most iconic trees in the world, the giant sequoia (Sequoiadendron giganteum). Spritella sequoiaphila gen. et sp. n. is described and illustrated and its status among other mycetophilid genera is analyzed and discussed.

Origin and diversification of the Milla Clade (Brodiaeoideae, Asparagaceae): a Neotropical group of six geophytic genera.

The Milla clade currently comprises six genera of geophytic plants distributed from Arizona to Guatemala. Three genera (Behria, Jaimehintonia and Petronymphe) are monotypic while the remaining genera (Bessera, Dandya and Milla) contain from two to ten (Milla) species. Parsimony, Maximum Likelihood and Bayesian Inference analyses were conducted with plastid and nuclear DNA sequences from a total of 181 plants belonging to 15 species in all six genera. Molecular dating was performed under a relaxed clock model. We examined the phylogenetic relationships of the genera and species, estimated origin-divergence times for the clade and genera and determined the ancestral distribution area of the clade by optimizing ancestral areas given current biogeographic distributions. The phylogenetic results suggest that final decisions on limits of the six genera in the Milla clade will have to be established until further taxonomic work is completed for Milla, in particular for the group of populations included under the name M. biflora. The later genus is rendered polyphyletic by other genera of the family. The origin of the Milla clade is estimated at 15.8Ma. Ancestral area of the clade most likely was located in the California Floristic Province and dispersal occurred most likely to the Chihuahuan-Coahuila Plateaus and the Trans-Mexican Volcanic Belt and from there to Baja California and the Sierra Madre del Sur. Two hypotheses that need further testing are proposed to explain complex relationships of genera and polyphyly of Milla, one in relation to fragmentation of populations and pollinator shifts and another suggesting that populations remained in refugia in the Trans-Mexican Volcanic Belt.

Phylogeography of Ramalina menziesii, a widely distributed lichen-forming fungus in western North America.

The complex topography and climate history of western North America offer a setting where lineage formation, accumulation and migration have led to elevated inter- and intraspecific biodiversity in many taxa. Here, we study Ramalina menziesii, an epiphytic lichenized fungus with a range encompassing major ecosystems from Baja California to Alaska to explore the predictions of two hypotheses: (i) that the widespread distribution of R. menziesii is due to a single migration episode from a single lineage and (ii) that the widespread distribution is due to the formation and persistence of multiple lineages structured throughout the species' range. To obtain evidence for these predictions, we first construct a phylogenetic tree and identify multiple lineages structured throughout the species' range--some ancient ones that are localized and other more recent lineages that are widely distributed. Second, we use an isolation with migration model to show that sets of ecoregion populations diverged from each other at different times, demonstrating the importance of historical and current barriers to gene flow. Third, we estimated migration rates among ecoregions and find that Baja California populations are relatively isolated, that inland California ecoregion populations do not send out emigrants and that migration out of California coastal and Pacific Northwest populations into inland California ecoregions is high. Such intraspecific geographical patterns of population persistence and dispersal both contribute to the wide range of this genetically diverse lichen fungus and provide insight into the evolutionary processes that enhance species diversity of the California Floristic Province.