Range edges and the molecular divergence of Greya moth populations

Aim We investigated the geographical pattern of genetic divergence and demographic history in the prodoxid moth Greya obscura throughout its entire geographical range in far western North America and compared it to the geographical patterns found in a previously studied species, Greya politella, which co‐occurs over the same range, in the same habitats, and on the same host plants. Location The study included sites distributed throughout the California Floristic Province. Methods We used analysis of cytochrome c oxidase subunit I (COI) and amplified fragment length polymorphisms to evaluate the pattern and history of genetic continuity among populations. Results Greya obscura populations show a history of spatial expansion with considerable haplotype diversity in the centre of the geographical range. As with G. politella, some range‐edge populations of G. obscura are sufficiently divergent (6.7% in COI) to be considered as potentially cryptic species. Greya obscura and G. politella, however, differ in the specific range‐edge sites showing greatest genetic divergence and cryptic speciation. Main conclusions These results corroborate the view that range edges are important cradles of divergence and speciation. In addition, the results indicate that the geographical pattern of divergence at edges may differ even among closely related species occupying the same habitats and using the same hosts.     

Limited phylogeographic structure in the flightless ground beetle, Calathus ruficollis, in southern California

The California Floristic Province is home to more than 8000 species of beetles, yet their geographical patterns of supra- and infraspecific diversity remain largely unexplored. In this paper, we investigate the phylogeography and population demographics of a flightless ground beetle, Calathus ruficollis (Coleoptera: Carabidae), in southern California. We sampled 136 specimens from 25 localities divided into 10 populations using a fragment of the mitochondrial cytochrome oxidase I gene. We tested several hypotheses, including the association of geography with particular clades and populations, the degree of differentiation among regions, and the expansion of populations. Parsimony and Bayesian phylogenetic analyses along with nested clade analysis and amova indicate a deep split between the southern Sierra Nevada population and populations south and west. This split corresponds closely to the split between subspecies C. ruficollis ignicollis (southern Sierra Nevada) and C. ruficollis ruficollis . Populations otherwise exhibit limited geographical structure, though F st values indicate some local differentiation. Mismatch distributions and Fu's F s indicate range expansion of several populations, suggesting that some structure may have been obscured by recent exchange. The population of C. ruficollis on Santa Cruz Island, which might have been expected to be isolated, shares several haplotypes with mainland populations, appearing to represent multiple colonizations.     

Systematics and evolution of Kibramoa Chamberlin 1924 (Araneae: Plectreuridae) from the California Floristic Province

The eight-eyed haplogyne spider family Plectreuridae Simon, 1893 is one of the oldest of spider families, currently comprising two genera (Kibramoa and Plectreurys), 30 extant species and one subspecies. Plectreuridae have not been rigorously examined since 1958, with only three new species added to Plectreurys. This study revisited a subset of taxa from the genus Kibramoa using a combined morphological and multilocus phylogenetic analysis. Species distribution modeling (SDM) was used to investigate the current and paleo distributional patterns of the genus Kibramoa throughout the biodiverse region of the California Floristic Province (CFP). A reexamination of genitalic morphology reflected cryptic species, yet multilocus Bayesian and maximum likelihood analyses of mitochondrial (COI, 16S) and nuclear (ITS1, 28S) markers consistently suggested several divergent lineages. A time-calibrated phylogeny indicated that the most recent common ancestor of Kibramoa appeared in the Mid-Miocene and continued to diversify throughout the Plio-Pleistocene. Xerophilic Kibramoa, as inferred by SDM, had a much wider distribution during the Mid-Holocene, when climate was at its warmest. This body of work uncovered novel findings regarding the evolution of plectreurids, provided the first phylogeny of the family, and demonstrated similar biogeographic patterns displayed in other CFP taxa.     

Phylogeography of the piranha genera Serrasalmus and Pygocentrus: implications for the diversification of the Neotropical ichthyofauna

The phylogenetic relationships within the piranhas were assessed using mitochondrial sequences with the aim of testing several hypotheses proposed to explain the origin of Neotropical diversity (palaeogeography, hydrogeology and museum hypotheses). Sequences of the ribosomal 16S gene (510 bp) and control region (980 bp) were obtained from 15 localities throughout the main South American rivers for 21 of the 28 extant piranha species. The results indicate that the genus Serrasalmus is monophyletic and comprises three major clades. The phylogeographical analyses of these clades allowed the identification of five vicariant events, extensive dispersal and four lineage duplications suggesting the occurrence of sympatric speciation. Biogeographical patterns are consistent with the prediction made by the museum hypothesis that lineages from the Precambrian shields are older than those from the lowlands of the Amazon. The vicariant events inferred here match the distribution of the palaeoarches and several postdispersal speciation events are identified, thereby matching the predictions of the palaeogeography and hydrogeology hypotheses, respectively. Molecular clock calibration of the control region sequences indicates that the main lineages differentiated from their most recent common ancestor at 9 million years ago in the proto Amazon-Orinoco and the present rate of diversification is the highest reported to date for large carnivorous Characiformes. The present results emphasize that an interaction among geology, sea-level changes, and hydrography created opportunities for cladogenesis in the piranhas at different temporal and geographical scales.     

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.     

Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province

The California Floristic Province harbours more endemic plant and animal taxa and more identifiable subspecies than any other area of comparable size in North America. We present evidence that physical historical processes have resulted in congruent patterns of genetic diversity over the past 2-10 million years. Using a molecular clock approach we show that diversification and establishment of spatial genetic structure across six taxonomic groups coincide with the putative age of California's mountain ranges and aridification in the region. Our results demonstrate the importance of geographical barriers and climatological events to species diversification and the overall geographical structure of biodiversity. These results should facilitate conservation efforts in this biodiversity hotspot for taxa whose population genetic structure is still unknown and may suggest the potential utility of this approach in regional conservation planning efforts.     

Regionalization of the avifauna of the Baja California Peninsula, Mexico: a parsimony analysis of endemicity and distributional modelling approach

Aim To analyse the distributional patterns of the Baja California Peninsula's resident avifauna, and to generate a regionalization based on a method that uses a parsimony analysis (parsimony analysis of endemicity, PAE) of point data and modelled potential distributions. Location The Baja California Peninsula, Mexico. Methods A data base was constructed containing records of 113 species of resident terrestrial birds present in the Baja California Peninsula. Records and localities were obtained from the literature and from specimens housed in scientific collections world‐wide. Raw data points and potential distribution maps obtained using the software Genetic Algorithms for Rule‐set Prediction (GARP), were analysed with PAE. Results The data base consisted of 4164 unique records (only one combination of species/locality) belonging to 113 terrestrial resident bird species, in a total of 809 localities. From the point distribution matrix, the analysis generated 500 equally parsimonious trees, from which a strict consensus cladogram with 967 steps was obtained. The cladogram shows a basal polytomy and some geographical correspondence of a few resolved groups obtained in the analysis. These results do not allow the recognition of areas defined by avifaunistic associations. From the potential distribution matrix, the analysis generated 501 equally parsimonious trees, and a strict consensus cladogram of 516 steps was obtained. The cladogram shows a higher resolution because of the number of resolved groups with better geographical correspondence and therefore regions are well‐defined. Main conclusions The correspondence of some groupings of species suggest their validity as areas with biogeographical (historical and/or ecological) meaning. This regionalization in the Baja California avifauna seems to be consistent with previous regionalizations for other groups. Hence, PAE is a useful tool for area categorization if reliable point records and prediction tools are available. Our results suggest that the geographical definition is much better using potential data generated by GARP, particularly when they are contrasted with the results from point data. Thus, this is an excellent alternative for developing biogeographical studies, as well as for improving the use of data from scientific collections and other sources of biodiversity information.     

Dispersal and diversification: macroevolutionary implications of the MacArthur–Wilson model, illustrated by Simulium (Inseliellum) Rubstov (Diptera: Simuliidae)

Aim Provide an empirical test of the ‘radiation zone’ hypothesis of the MacArthur–Wilson theory of island biogeography using the taxon‐pulse hypothesis of Erwin and Brooks Parsimony Analysis (BPA) on Simulium (Inseliellum) Rubstov. Location Micronesia, Cook Islands, Austral Islands, Society Islands, Marquesas Islands, Fiji and New Caledonia. Methods Primary and secondary BPA of the phylogeny of Inseliellum. Results Primary BPA showed that 15% of the taxon area cladogram contained area reticulations. Secondary BPA (invoking the area duplication convention) generated a clear sequence of dispersal for Inseliellum. The sequence follows a Micronesia – Cook Islands – Marquesas Islands – Society Islands dispersal, with a separate dispersal from the Cook Islands to the Austral Islands less than 1 Ma. A radiation in the island of Tahiti (Society Islands) produced numerous dispersals from Tahiti to other islands within the Society Islands system. Islands close to Tahiti (source island) have been colonized from Tahiti more often than islands far from Tahiti, but a higher proportion of those species colonizing distant islands have become distinct species. Main conclusions The dispersal sequence of Inseliellum exhibits both old to young island dispersal and young to old island dispersal. This is due to habitat availability on each island. Inseliellum is a model system in exemplifying the ‘radiation zone’ hypothesis of MacArthur and Wilson. As well, islands close to the source are colonized more often that those far from the source, but colonization of islands far away from the source results in a higher proportion of speciation events than for islands close to the source. The diversification of Inseliellum corresponds to a taxon‐pulse radiation, with a centre of diversification on Tahiti resulting from its large area and abundant freshwater habitats. This study illustrates the utility of BPA in identifying complex scenarios that can be used to test theories about the complementary roles of ecology and phylogeny in historical biogeography.     

Testing the ‘Pleistocene species pump’ in alpine habitats: lineage diversification of flightless ground beetles (Coleoptera: Carabidae: Nebria) in relation to altitudinal zonation

Alpine species often have similar demographic responses to Pleistocene climate changes, but exhibit different spatial patterns of genetic diversity. Using a comparative phylogeographical approach, we examined the factors influencing lineage formation in three alpine carabid beetles of the genus Nebria Latreille inhabiting the California Sierra Nevada. These flightless beetles differ in altitudinal zonation and habitat preferences, but overlap spatially, have limited dispersal capacities and share life history characteristics. Species distribution modelling predicted decreasing population connectivity in relation to increasing altitudinal preferences. Diversity patterns at the cytochrome oxidase subunit I gene revealed north–south genetic structure and recent population growth in all three species. The high‐elevation‐restricted species, Nebria ingens Horn, exhibited a deep phylogeographical split, morphological divergence and evidence of limited, unidirectional gene flow towards the south. This was supported by additional data from three nuclear genes and isolation with migration analysis. Nebria spatulata Van Dyke, inhabiting an intermediate altitudinal range, exhibited fixed morphological differences between northern and southern populations, but showed limited structure. The broadly distributed Nebria ovipennis LeConte showed less structure and lacked morphological variation. Diversification of these Nebria species supports the role of altitudinal zonation in lineage formation and is consistent with the Pleistocene species pump model. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco

Pleistocene glacial cycles are thought to have played a major role in the diversification of temperate and boreal species of North American birds. Given that coalescence times between sister taxa typically range from 0.1 to 2.0 Myr, it has been assumed that diversification occurred as populations were isolated in refugia over long periods of time, probably spanning one to several full glacial cycles. In contrast, the rapid postglacial range expansions and recolonization of northern latitudes following glacial maxima have received less attention as potential promoters of speciation. Here we report a case of extremely rapid diversification in the songbird genus Junco as a result of a single continent-wide range expansion within the last 10 000 years. Molecular data from 264 juncos sampled throughout their range reveal that as the yellow-eyed junco (Junco phaeonotus) of Mesoamerica expanded northward following the last glacial maximum, it speciated into the dark-eyed junco (Junco hyemalis), which subsequently diversified itself into at least five markedly distinct and geographically structured morphotypes in the USA and Canada. Patterns of low genetic structure and diversity in mitochondrial DNA and amplified fragment length polymorphism loci found in dark-eyed juncos relative to Mesoamerican yellow-eyed juncos provide support for the hypothesis of an expansion from the south, followed by rapid diversification in the north. These results underscore the role of postglacial expansions in promoting diversification and speciation through a mechanism that represents an alternative to traditional modes of Pleistocene speciation.     

Genetic variation among Corsican and continental populations of the Eurasian treecreeper (Aves: Certhia familiaris) reveals the existence of a palaeoendemic mitochondrial lineage

In this study we investigated the phylogenetics of the Eurasian treecreeper (Certhia familiaris), a forest passerine with a wide Palaearctic range including Corsica, using three mitochondrial genes and three nuclear introns, and its phylogeographic history using the COI gene. Our phylogenetic results, including eight of the ten sub‐species currently recognized, support the monophyly of C. familiaris with respect to its Indo‐Asian sister species C. hodgsoni. C. familiaris comprises two lineages that diverged during the mid‐Pleistocene (c. 1 Myr): one palaeoendemic lineage has an allopatric range nowadays restricted to the Corsica island and the Caucasus region whereas the second one, more recent and widespread, is distributed over most of Eurasia and in northern China. The most likely scenario that may explain such a pattern is a double colonization of the western Palaearctic from the eastern range of the species. During the middle Pleistocene period, a first lineage expanded its range up into Europe but did not persist through glacial cycles except in Corsica and the Caucasus region. Later, during the upper Pleistocene, a second lineage began to diversify around 0.09 Myr, spreading towards the western Palaearctic from a unique refuge likely located in the eastern Palaearctic [correction added on 6 March 2015 after first online publication: 0.9 Myr amended to 0.09 Myr]. Apart from C. f. corsa, our results do not suggest any distinct evolutionary history for other sub‐species previously described on morphological grounds in Europe. Our study highlights the important conservation value of the Corsican treecreeper and emphasizes the major role of mature pine forests in the evolution of endemic bird taxa in Corsica. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 134–153.     

The evolution of sexual and parthenogenetic Warramaba: a window onto Plio–Pleistocene diversification processes in an arid biome

Environmental changes over the Plio‐Pleistocene have been key drivers of speciation patterns and genetic diversification in high‐latitude and mesic environments, yet comparatively little is known about the evolutionary history of species in arid environments. We applied phylogenetic and phylogeographic analyses to understand the evolutionary history of Warramaba grasshoppers from the Australian arid zone, a group including sexual and parthenogenetic lineages. Sequence data (mitochondrial COI) showed that the four major sexual lineages within Warramaba most likely diverged in the Pliocene, around 2–7 million years ago. All sexual lineages exhibited considerable phylogenetic structure. Detailed analyses of the hybrid parthenogenetic species W. virgo and its sexual progenitors showed a pattern of high phylogenetic diversity and phylogeographic structure in northern lineages, and low diversity and evidence for recent expansion in southern lineages. Northern sexual lineages persisted in localized refugia over the Pleistocene, with sustained barriers promoting divergence over this period. Southern parts of the present range became periodically unsuitable during the Pleistocene, and it is into this region that parthenogenetic lineages have expanded. Our results strongly parallel those for sexual and parthenogenetic lineages of the gecko Heteronotia from the same region, indicating a highly general effect of Plio‐Pleistocene environmental change on diversification processes in arid Australia.     

Phylogeography of the mountain chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change

Since the late 1990s, molecular techniques have fuelled debate about the role of Pleistocene glacial cycles in structuring contemporary avian diversity in North America. The debate is still heated; however, there is widespread agreement that the Pleistocene glacial cycles forced the repeated contraction, fragmentation, and expansion of the North American biota. These demographic processes should leave genetic 'footprints' in modern descendants, suggesting that detailed population genetic studies of contemporary species provide the key to elucidating the impact of the late Quaternary (late Pleistocene-Holocene). We present an analysis of mitochondrial DNA (mtDNA) variation in the mountain chickadee (Poecile gambeli) in an attempt to examine the genetic evidence of the impact of the late Quaternary glacial cycles. Phylogenetic analyses reveal two strongly supported clades of P. gambeli: an Eastern Clade (Rocky Mountains and Great Basin) and a Western Clade (Sierra Nevada and Cascades). Post-glacial introgression is apparent between these two clades in the Mono Lake region of Central California. Within the Eastern Clade there is evidence of isolation-by-distance in the Rocky Mountain populations, and of limited gene flow into and around the Great Basin. Coalescent analysis of genetic variation in the Western Clade indicates that northern (Sierra Nevada/Cascades) and southern (Transverse/Peninsular Ranges) populations have been isolated and evolving independently for nearly 60,000 years.     

Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

Understanding the evolutionary history of the species in a particular region provides insights into how that fauna was formed. Of particular interest to biogeographers is examining the impact a geographical barrier had in generating temporal genetic diversity among codistributed species. We examined the impact a major New World barrier, the Isthmus of Tehuantepec (IT) in southern Mexico, had on a regional bird fauna. Specifically, genetic data from 10 montane-forest bird taxa were analysed using approximate Bayesian computation (ABC) to test the hypothesis of simultaneous intraspecific diversification at the IT. Because effective population size (N_e) has the greatest impact on coalescent times, thereby affecting tests of divergence among codistributed taxa, we chose priors for both current and ancestral N_e using empirical estimates of theta. The ABC method detected two discrete diversification events. Subsequent analysis with the number of diversification events constrained to two suggests that four taxa diverged in an older event, with the remaining six diverging more recently. Application of a range of mutation rates from 2.0 to 5.0% Myr⁻¹ places both events within the Pleistocene or Late Pliocene, suggesting that fluctuations in montane habitat induced by climate cycles and a late Pliocene seaway may have fractured this montane bird fauna. The results presented here suggest this avian fauna responded in a relatively concerted fashion over the last several million years.     

The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense

A primary goal of conservation genetics is the discovery, delimitation and protection of phylogenetic lineages within sensitive or endangered taxa. Given the importance of lineage protection, a combination of phylogeography, historical geology and molecular clock analyses can provide an important historical context for overall species conservation. We present the results of a range-wide survey of genetic variation in the California tiger salamander, Ambystoma californiense, as well as a summary of the past several million years of inundation and isolation of the Great Central Valley and surrounding uplands that constitute its limited range. A combination of population genetic and phylogenetic analyses of mitochondrial DNA variation among 696 samples from 84 populations revealed six well-supported genetic units that are geographically discrete and characterized by nonoverlapping haplotype distributions. Populations from Santa Barbara and Sonoma Counties are particularly well differentiated and geographically isolated from all others. The remaining units in the Southern San Joaquin Valley, Central Coast Range, Central Valley and Bay Area are separated by geological features, ecological zone boundaries, or both. The geological history of the California landscape is consistent with molecular clock evidence suggesting that the Santa Barbara unit has been isolated for at least 0.74-0.92 Myr, and the Sonoma clade is equally ancient. Our work places patterns of genetic differentiation into both temporal- and landscape-level contexts, providing important insights into the conservation genetics of the California tiger salamander.     

Phylogeography recapitulates topography: very fine-scale local endemism of a saproxylic 'giant' springtail at Tallaganda in the Great Dividing Range of south-east Australia

Comparative phylogeography can reveal processes and historical events that shape the biodiversity of species and communities. As part of a comparative research program, the phylogeography of a new, endemic Australian genus and species of log-dependent (saproxylic) collembola was investigated using mitochondrial sequences, allozymes and anonymous single-copy nuclear markers. We found the genetic structure of the species corresponds with five a priori microbiogeographical regions, with population subdivision at various depths owing to palaeoclimatic influences. Closely related mtDNA haplotypes are codistributed within a single region or occur in adjacent regions, nuclear allele frequencies are more similar among more proximate populations, and interpopulation migration is rare. Based on mtDNA divergence, a late Miocene-late Pliocene coalescence is likely. The present-day distribution of genetic diversity seems to have been impacted by three major climatic events: Pliocene cooling and drying (2.5-7 million years before present, Mybp), early Pleistocene wet-dry oscillations (c. 1.2 Mybp) and the more recent glacial-interglacial cycles that have characterized the latter part of the Quaternary (<0.4 Mybp).     

The discordance of diversification: evolution in the tropical‐montane frogs of the Eastern Arc Mountains of Tanzania

Species with similar geographical distribution patterns are often assumed to have a shared biogeographical history, an assumption that can be tested with a combination of molecular, spatial, and environmental data. This study investigates three lineages of Hyperolius frogs with concordant ranges within the Eastern Afromontane Biodiversity Hotspot to determine whether allopatric populations of co‐distributed lineages shared a parallel biogeographical response to their shared paleoclimatic histories. The roles of refugial distributions, isolation, and climate cycles in shaping their histories are examined through Hierarchical Approximate Bayesian Computation, comparative phylogeography, and comparisons of current and past geographical distributions using ecological niche models. Results from these analyses show these three lineages to have independent evolutionary histories, which current spatial configurations of sparsely available habitat (montane wetlands) have moulded into convergent geographical ranges. In spite of independent phylogeographical histories, diversification events are temporally concentrated, implying that past vicariant events were significant at the generic level. This mixture of apparently disparate histories is likely due to quantifiably different patterns of expansion and retreat among species in response to past climate cycles. Combining climate modelling and phylogeographical data can reveal unrecognized complexities in the evolution of co‐distributed taxa.     

Following the rivers: historical reconstruction of California voles Microtus californicus (Rodentia: Cricetidae) in the deserts of eastern California

The California vole, Microtus californicus, restricted to habitat patches where water is available nearly year‐round, is a remnant of the mesic history of the southern Great Basin and Mojave deserts of eastern California. The history of voles in this region is a model for species‐edge population dynamics through periods of climatic change. We sampled voles from the eastern deserts of California and examined variation in the mitochondrial cytb gene, three nuclear intron regions, and across 12 nuclear microsatellite markers. Samples are allocated to two mitochondrial clades: one associated with southern California and the other with central and northern California. The limited mtDNA structure largely recovers the geographical distribution, replicated by both nuclear introns and microsatellites. The most remote population, Microtus californicus scirpensis at Tecopa near Death Valley, was the most distinct. This population shares microsatellite alleles with both mtDNA clades, and both its northern clade nuclear introns and southern clade mtDNA sequences support a hybrid origin for this endangered population. The overall patterns support two major invasions into the desert through an ancient system of riparian corridors along streams and lake margins during the latter part of the Pleistocene followed by local in situ divergence subsequent to late Pleistocene and Holocene drying events. Changes in current water resource use could easily remove California voles from parts of the desert landscape.