Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria)

Amanita muscaria sensu lato has a wide geographic distribution, occurring in Europe, Asia, Africa, Australia, New Zealand, and North, Central and South America. Previous phylogenetic work by others indicates three geographic clades (i.e. 'Eurasian', 'Eurasian-alpine' and 'North American' groups) within A. muscaria. However, the historical dispersal patterns of A. muscaria remained unclear. In our project, we collected specimens from arctic, boreal and humid temperate regions in Alaska, and generated DNA sequence data from the protein-coding beta-tubulin gene and the internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal DNA repeat. Homologous sequences from additional A. muscaria isolates were downloaded from GenBank. We conducted phylogenetic and nested clade analyses (NCA) to reveal the phylogeographic history of the species complex. Although phylogenetic analyses confirmed the existence of the three above-mentioned clades, representatives of all three groups were found to occur sympatrically in Alaska, suggesting that they represent cryptic phylogenetic species with partially overlapping geographic distributions rather than being allopatric populations. All phylogenetic species share at least two morphological varieties with other species, suggesting ancestral polymorphism in pileus and wart colour pre-dating their speciations. The ancestral population of A. muscaria likely evolved in the Siberian-Beringian region and underwent fragmentation as inferred from NCA and the coalescent analyses. The data suggest that these populations later evolved into species, expanded their range in North America and Eurasia. In addition to range expansions, populations of all three species remained in Beringia and adapted to the cooling climate.     

Timing of the population dynamics of bullhead Cottus gobio (Teleostei: Cottidae) during the Pleistocene

Abstract Pleistocene genetic structure of the bullhead, Cottus gobio, was evaluated across the western Palearctic using a 771‐bp long fragment of the mitochondrial control region in 123 individuals collected at 35 sites (data set I). In total, 59 haplotypes that differed at 73 positions (9.3%) were detected. Data analysis also included sequences from Englbrecht et al. (2000 ), thus increasing the sampling to a more comprehensive data set of 529 fish and 63 control region sequences of 482 bp (data set II). A minimum spanning and phylogenetic tree identified a seventh clade (Brittany–Loire) in addition to the previously identified six clades. The geographical range of the North Sea and Lower Rhine clades was considerably larger than thought previously. Haplotype diversity was generally low, and the total fixation index high (F_ST = 0.49). Among‐group differentiation accounted for 41.7% (data set I) of the variation. Contiguous range expansions and restricted gene flow combined with isolation by distance, interspersed with past fragmentation characterize bullhead across its range. New is the knowledge that dated interglacial periods correlated with population expansions; river captures, proglacial lake systems and sea level played a significant role in the dispersal and expansion either in northern or southern direction. Hence it became possible to identify and date the colonization routes and putative palaeorefugia, most of which were located in Central and North‐west Europe. Glacial periods resulted in distinct fragmentation events and lineage sorting.     

A phylogeographic analysis of populations of the wood turtle (Glyptemys insculpta) throughout its range

We investigated the phylogeography of wood turtles, Glyptemys insculpta, in North America using 750 bp of the mitochondrial control region from 117 individuals sampled at 29 localities across the species' range. A total of 21 haplotypes were identified and little genetic variation was found. The highest pairwise difference was 2%. From nested clade analysis (NCA), one main postglacial dispersal route was inferred along the east coast, with subsequent westward dispersal. NCA further revealed some patterns of restricted gene flow/dispersal. We propose that wood turtles experienced a combined effect of bottleneck during the Pleistocene as well as of selective sweep, which produced the low level of variation observed. Following the Pleistocene, wood turtles would have undergone a rapid northward expansion from a common southern refugium as glaciers retreated. These findings shed light on where to direct conservation priorities, on conservation strategies needed, and on the potential effects of interpopulation transfers for this vulnerable species.     

Phylogeography of Caribbean lizard malaria: tracing the history of vector‐borne parasites

The Anolis lizards of the eastern Caribbean islands are parasitized by several species of malaria parasites (Plasmodium). Here I focus on two species of Plasmodium, using molecular data (mitochondrial cytochrome b sequences) to recover the phylogeography of the parasites throughout the Lesser Antilles and Puerto Rico. The two parasites were originally described as a single species, P. azurophilum, which infects both red and white blood cells. Here the two species are termed P. azurophilum Red and P. azurophilum White based on their host cell type. Six haplotypes were found in 100 infections sequenced of P. azurophilum Red and six in 45 infections of P. azurophilum White. Nested clade analysis revealed a significant association of geographical location and clades as well as a pattern of past fragmentation of parasite populations. This is consistent with the hypothesis that vector‐borne parasites such as malaria may be subject to frequent local extinctions and recolonizations. Comparison of the phylogeography of the lizard and parasites shows only weak concordance; that is, the parasites colonized the lizards in the islands, but dispersal events between islands via vectors or failed lizard colonizations were present. The two parasites had different histories, P. azurophilum Red colonized the islands from both the north and south, and P. azurophilum White originated in the central Lesser Antilles, probably from P. azurophilum Red, then moved to both north and south. This is the first study to examine the biogeography of a pair of sibling species of vector‐borne parasites within an island archipelago system.     

autoinfer1.0: a computer program to infer biogeographical events automatically

autoinfer is a computer program for biogeographical inference based on nested clade analysis. To reduce the obscurity caused by manual inference, we defined geographically concordant clades and intermediate geographical areas between two clades. The program will perform most of the inferences automatically with a minimum of input from the user. We believe that autoinfer will save much time for the user compared with using the inference key by hand and, furthermore, will reduce the errors of inference resulting from different criteria in deduction.     

Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickens

Current methods of DNA sequence analysis attempt to reconstruct historical patterns of population structure and growth from contemporary samples. However, these techniques may be influenced by recent population bottlenecks, which have the potential to eliminate lineages that reveal past changes in demography. One way to examine the performance of these demographic methods is to compare samples from populations before and after recent bottlenecks. We compared estimates of demographic history from populations of greater prairie-chickens (Tympanuchus cupido) before and after recent bottlenecks using four common methods (nested clade analysis [NCA], Tajima's D, mismatch distribution, and MDIV). We found that NCA did not perform well in the presence of bottleneck events, although it did recover some genetic signals associated with increased isolation and the extinction of intermediate populations. The majority of estimates for Tajima's D, including those from bottlenecked populations, were not significantly different from zero, suggesting our data conformed to neutral expectations. In contrast, mismatch distributions including the raggedness index were more likely to identify recently bottlenecked populations with this data set. Estimates of population mutation rate (theta), population divergence time (t), and time to the most recent common ancestor (TMRCA) from MDIV were similar before and after bottlenecks; however, estimates of gene flow (M) were significantly lower in a few cases following a bottleneck. These results suggest that caution should be used when assessing demographic history from contemporary data sets, as recently fragmented and bottlenecked populations may have lost lineages that affect inferences of their demographic history.     

Molecular evidence for sequential colonization and taxon cycling in freshwater decapod shrimps on a Caribbean island

Taxon cycling, i.e. sequential phases of expansions and contractions in species' distributions associated with ecological or morphological shifts, are postulated to characterize dynamic biogeographic histories in various island faunas. The Caribbean freshwater shrimp assemblage is mostly widespread and sympatric throughout the region, although one species (Atyidae: Atya lanipes) is geographically restricted and ecologically and morphologically differentiated from other Atya species. Using patterns of nucleotide variation at the COI mtDNA gene in five species of freshwater shrimp (A. lanipes, A. scabra, A. innocuous; Xiphocarididae: Xiphocaris elongata; Palaemonidae: Macrobrachium faustinum) from Puerto Rico, we expected to detect a signature of sequential colonization in these shrimp, consistent with the concept of taxon cycling, and expected that A. lanipes would be at a different taxon stage (i.e. an early stage species) to all other species. We also examined patterns of genetic population structure in each species expected with poor, intermediate and well-developed abilities for among-river dispersal. Population expansions were detected in all species, although the relative timing of the expansions varied among them. Assuming that population expansions followed colonization of Puerto Rico by freshwater shrimp, results bear the hallmarks of sequential colonization and taxon cycling in this fauna. A. lanipes had a star phylogeny, low mean pairwise nucleotide differences and recent (Holocene) estimates for an in situ population expansion in Puerto Rico, and it was inferred as an early stage species in the taxon cycle undergoing a secondary phase of expansion. All other species were inferred as late stage species undergoing regional population expansions, as their mean pairwise nucleotide differences were relatively high and phylogenetic patterns were more complex than A. lanipes. High rates of gene flow without isolation by distance among rivers were detected in all species, although results should be treated cautiously as some populations are unlikely to be in mutation-drift equilibrium. Nested clade analysis produced inconsistent results among species that all have high rates of gene flow and expanding populations.     

Historical perspectives on population genetics and conservation of three marine turtle species

Considerable phylogeographic and population genetic research has been conducted on marine turtles. Less attention, however, has been paid to the historical patterns and processes that have led to present patterns of genetic structure, and particularly, how these populations have responded to major climatic changes in the past. To address these questions, we analyzed previously published mitochondrial haplotype data independently for three marine turtle species, the loggerhead (Caretta caretta), hawksbill (Eretmochelys imbricata), and green turtle (Chelonia mydas). Considering all three species, we conducted analyses on a total of 657 individuals from 36 nesting beaches in the Atlantic and Mediterranean. Our results suggest that much of the contemporary genetic structure has been significantly affected by complex patterns of historical population subdivision, long-distance dispersal, and restricted geneflow. These inferences also imply that the climatic and sea level fluctuations during the Pleistocene may have had contrasting effects on genetic structure (e.g., fragmenting versus homogenizing) and on population sizes. Estimates of historical and current effective population sizes further highlight differential demographic responses across species to historical climatic cycles. Collectively, our results provide evidence for the occurrence of historical refugia through climatic cycles and complex historical metapopulation dynamics, and identify common and unique patterns of metapopulation structure across species. These historical patterns provide a basis for predictive estimates of metapopulation responses to habitat loss, population extirpation, and global climatic change.     

Sea‐level changes and palaeo‐ranges: reconstruction of ancient shorelines and river drainages and the phylogeography of the Australian land crayfish Engaeus sericatus Clark (Decapoda: Parastacidae)

Historical sea levels have been influential in shaping the phylogeography of freshwater‐limited taxa via palaeodrainage and palaeoshoreline connections. In this study, we demonstrate an approach to phylogeographic analysis incorporating historical sea‐level information in a nested clade phylogeographic analysis (NCPA) framework, using burrowing freshwater crayfish as the model organism. Our study area focuses on the Bass Strait region of southeastern Australia, which is marine region encompassing a shallow seabed that has emerged as a land bridge during glacial cycles connecting mainland Australia and Tasmania. Bathymetric data were analysed using Geographical Information Systems (GIS) to delineate a palaeodrainage model when the palaeocoastline was 150 m below present‐day sea level. Such sea levels occurred at least twice in the past 500 000 years, perhaps more often or of larger magnitude within the last 10 million years, linking Victoria and Tasmania. Inter‐locality distance measures confined to the palaeodrainage network were incorporated into an NCPA of crayfish (Engaeus sericatus Clark 1936) mitochondrial 16S rDNA haplotypes. The results were then compared to NCPAs using present‐day river drainages and traditional great‐circle distance measures. NCPA inferences were cross‐examined using frequentist and Bayesian procedures in the context of geomorphological and historical sea‐level data. We found distribution of present‐day genetic variation in E. sericatus to be partly explained not only by connectivity through palaeodrainages but also via present‐day drainages or overland (great circle) routes. We recommend that future studies consider all three of these distance measures, especially for studies of coastally distributed species.     

Subterranean archipelago in the Australian arid zone: mitochondrial DNA phylogeography of amphipods from central Western Australia

In 1998, a unique subterranean ecosystem was discovered in numerous isolated calcrete (carbonate) aquifers in the arid Yilgarn region of Western Australia. Previous morphological and genetic analyses of a subterranean water beetle fauna suggest that calcrete aquifers are equivalent to closed island habitats that have been isolated for millions of years. We tested this hypothesis further by phylogeographic analyses of subterranean amphipods (Crangonyctoidea: Paramelitidae and Hyalidae) using mitochondrial DNA sequence data derived from the cytochrome oxidase I gene. Phylogenetic analyses and population genetic analyses (samova) provided strong evidence for the existence of at least 16 crangonyctoid and six hyalid divergent mitochondrial lineages, each restricted in their distribution to a single calcrete aquifer, in support of the 'subterranean island (archipelago) hypothesis' and extending its scope to include entirely water respiring invertebrates. Sequence divergence estimates between proximate calcrete populations suggest that calcretes have been isolated at least since the Pliocene, coinciding with a major aridity phase that led to the intermittent drying of surface water. The distribution of calcretes along palaeodrainage channels and on either side of drainage divides, have had less influence on the overall phylogeographic structure of populations, with evidence that ancestral crangonyctoid and hyalid species moved between catchments multiple times prior to their isolation within calcretes. At least two potential modes of evolution may account for the diversity of subterranean amphipod populations: dispersal/vicariance of stygobitic species or colonization of calcretes by surface species and independent evolution of stygobitic characteristics.     

European colonization by the spined loach (Cobitis taenia) from Ponto-Caspian refugia based on mitochondrial DNA variation

In the last 20 years, new species, asexual reproduction, polyploidy and hybridization have all been reported within the genus Cobitis. An understanding of the current distribution and baseline phylogeographical history of 'true' nonhybrid Cobitis species is crucial in order to unravel these discoveries. In the present work, we investigated the phylogeography of the spined loach, Cobitis taenia, using 1126 bp of the mitochondrial cytochrome b gene from 174 individuals collected at 47 sites. In total, 51 haplotypes that differed at 49 positions (4.35%) were detected. We deduce that C. taenia survived European glaciations in at least three refugees in the Ponto-Caspian area. Two of these refugees each provided a major lineage that recolonized Europe in separate directions: one westward to England and the other spreading north into Russia before moving west. A third (minor) lineage that contributed little to the recolonization of Europe was also revealed--remaining near its Black Sea refuge. However, more recent history was difficult to resolve with colonization from a more western refugium during the last glacial maximum (LGM) a distinct possibility. Nested clade analysis indicates a pattern of restricted gene flow with isolation by distance at the first two levels and overall. Unlike many other European freshwater fish species, the Danube is not part of the current distribution of C. taenia, nor was it used as either a refuge or a source of colonization of Europe. Low genetic diversity within C. taenia suggests that its colonization of Europe is relatively recent. Demographic analyses revealed a history of recent expansion and isolation by distance.     

Pan-European phylogeography of the aquatic snail Theodoxus fluviatilis (Gastropoda: Neritidae)

Investigating the geographical distribution of genetic lineages within species is critical to our understanding of how species evolve. As many species inhabit large and complex ranges, it is important that phylogeographical research take into account the entire range of widespread species to clarify how myriad extrinsic variables have affected their evolutionary history. Using phylogenetic, nested clade, and mismatch distribution analyses on a portion of the mitochondrial COI gene, I demonstrate that the wide-ranging freshwater snail Theodoxus fluviatilis possesses in parallel many of the phylogeographical patterns seen in less widespread freshwater species of Europe. Fragmentary forces play a major part in structuring the range of this species, with 12 of 14 geographically structured nested clades displaying a distribution consistent with fragmentation or restricted dispersal. Certain regions of southern Europe harbour the majority of genetic diversity (total haplotype diversity, H = 0.87), particularly Italy (H = 0.87) and areas surrounding the Black Sea (H = 0.81). Post-Pleistocene range expansion is pronounced, with the majority of northern European populations (95% of sample sites) having arisen from northern Italian individuals that initially colonized northern Germany. Additionally, two highly divergent haplotype lineages present in northern Germany imply that there were at least two postglacial recolonization routes. Estuaries may also provide a means of dispersal given that no genetic differentiation was found between estuarine populations and neighbouring freshwater populations. Taken together, these data reveal a species with a complex genetic history resulting from the fragmentary effects of European geology as well as continuous and discrete range expansion related to their aquatic biology.     

Genetic structure of the star sea squirt, Botryllus schlosseri, introduced in southern European harbours

The introduction of new genetic variants or species is often caused by maritime transport between harbours. Botryllus schlosseri is a cosmopolitan ascidian species that is found in both harbours and open shore habitats. In order to determine the influence of ship traffic on the genetic structure and phylogeography of B. schlosseri in southern Europe, we analyzed the variability of a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI). We sampled seven Atlanto-Mediterranean harbour populations and three open-shore populations. In addition, we sequenced some colonies from the US-Atlantic coast and from other Mediterranean localities to perform phylogenetic analyses. Although the number of polymorphic sites recorded (25.8%) was within the range observed in other population studies based on ascidian COI sequences, the haplotypic diversity (16 haplotypes out of 181 sequences) was much lower. Moreover, a lack of intermediate haplotypes was observed. This pattern of high nucleotide diversity and low haplotype diversity was consistent with introduction events of a few divergent haplotypes. We found a strong genetic structure in the study populations. Gene flow was only appreciable between some harbour populations. Harbour- and open-shore populations were well differentiated, although there was no evidence for isolation by distance. A nested clade analysis pointed to long-distance colonization, possibly coupled with subsequent fragmentation, as the underlying process. Our results suggest that B. schlosseri entered the study area via harbour-hopping, possibly through recurrent introduction events. The haplotypes from North America and most of the European ones were grouped in the same phylogenetic clade. This suggests occasional gene flow between both continents, probably through ship transport.     

Determining the origin and age of the Westland beech (Nothofagus) gap, New Zealand, using fungus beetle genetics

The formation and maintenance of the Nothofagus beech gap in the South Island, New Zealand, has been the focus of biogeographical debate since the 1920s. We examine the historical process of gap formation by investigating the population genetics of fungus beetles: Brachynopus scutellaris (Staphylinidae) inhabits logs and is absent from the beech gap, and Hisparonia hystrix (Nitidulidae) is contiguous through the gap and is found commonly on sooty mould growing on several plant species. Both species show distinctive northern and southern haplotype distributions while H. hystrix recolonized the gap as shown by definitive mixing. B. scutellaris shows two major haplotype clades with strong geographical concordance, and unlike H. hystrix, has clearly defined lineages that can be partitioned for molecular dating. Based on coalescence dating methods, disjunct lineages of B. scutellaris indicate that the gap was formed less than 200 000 years ago. Phylogenetic imprints from both species reveal similar patterns of population divergence corresponding to recent glacial cycles, favouring a glacial explanation for the origin of the gap. Post-gap colonization by H. hystrix may have been facilitated by the spread of Leptospermum scoparium host trees to the area, and they may be better at dispersing than B. scutellaris which may be constrained by fungal host and/or microhabitat. The gap-excluded species B. scutellaris is found in both beech and podocarp-broadleaf forests flanking the Westland gap and its absence in the gap may be related to incomplete recolonization following glacial retreat. We also discuss species status and an ancient polymorphism within B. scutellaris .     

A Second Look at Mitochondrial DNA Variability in European Anchovy (Engraulis encrasicolus): Assessing Models of Population Structure and the Black Sea Isolation Hypothesis

Genetic architectures of marine fishes are generally shallow because of the large potential for gene flow in the sea. European anchovy, however, are unusual among small pelagic fishes in showing large differences among sub-basins and in harbouring two mtDNA phylogroups (‘A’ & ‘B’), representing 1.1–1.85 million years of separation. Here the mtDNA RFLP dataset of Magoulas et al. [1996, Mol. Biol. Evol. 13: 178–190] is re-examined to assess population models accounting for this subdivided population structure and to evaluate the zoogeographical origins of the two major phylogroups. Haplotype and nucleotide diversities are highest in the Ionian Sea and lowest in the Aegean and Black seas. However, this gradient is absent when ‘A’ and ‘B’ haplotypes are examined separately. Neither the self-sustaining nor the basin population models adequately describe anchovy population behaviour. Tests for neutrality, mismatch and nested clade analyses are concordant in depicting recent expansions of both phylogroups. Unimodel mismatch distributions and haplotype coalescences dating to the last (Eemian) interglacial (‘B’) and the Weichselian pleniglacial period (‘A’) indicate separate colonizations of the Mediterranean Basin. Phylogroup ‘A’ is unlikely to have arisen through continuous long-term isolation in the Black Sea because of climate extremes from displaced subpolar weather systems during the ice ages. Ancestors of both groups appear to have colonized the Mediterranean from the Atlantic in the late Pleistocene. Hence, zoogeographic models of anchovy in the Mediterranean must also include the eastern (and possibly southern) Atlantic.     

Catchments catch all: long-term population history of a giant springtail from the southeast Australian highlands--a multigene approach

Phylogeography can reveal evolutionary processes driving natural genetic-geographical patterns in biota, providing an empirical framework for optimizing conservation strategies. The long-term population history of a rotting-log-adapted giant springtail (Collembola) from montane southeast Australia was inferred via joint analysis of mitochondrial and multiple nuclear gene genealogies. Contemporary populations were identified using multilocus nuclear genotype clustering. Very fine-scale sampling combined with nested clade and coalescent-based analyses of sequences from mitochondrial cytochrome oxidase I and three unlinked nuclear loci uncovered marked population structure, deep molecular divergences, and abrupt phylogeographical breaks over distances on the order of tens of kilometres or less. Despite adaptations that confer low mobility, rare long-distance gene flow was implicated: novel computer simulations that jointly modelled stochasticity inherent in coalescent processes and that of DNA sequence evolution showed that incomplete lineage sorting alone was unable to explain the observed spatial-genetic patterns. Impacts of Pleistocene or earlier climatic cycles were detected on multiple timescales, and at least three putative moist forest refuges were identified. Water catchment divisions predict phylogeographical patterning and present-day population structure with high precision, and may serve as an excellent surrogate for biodiversity indication in sedentary arthropods from topographically heterogeneous montane temperate forests.