Testing the effect of transient Plio‐Pleistocene barriers in monsoonal Australo‐Papua: did mangrove habitats maintain genetic connectivity in the Black Butcherbird?

Changes in climate and sea level are hypothesized to have promoted the diversification of biota in monsoonal Australia and New Guinea by causing repeated range disjunctions and restricting gene flow between isolated populations. Using a multilocus (one mtDNA locus, five nuclear introns) phylogeographic approach, we test whether populations of the mangrove and rainforest restricted Black Butcherbird (Cracticus quoyi) have diverged across several geographic barriers defined a priori for this region. Phylogeographic structure and estimates of divergence times revealed Plio-Pleistocene divergences and long-term restricted gene flow of populations on either side of four major geographic barriers between and within Australia and New Guinea. Overall, our data are consistent with the hypothesis that mesic-adapted species did not disperse across the open dry woodlands and grasslands that dominated the transient palaeo-landbridges during the Plio-Pleistocene despite the presence of mangrove forests that might have acted as dispersal corridors for mesic-adapted species. Our study offers one of the first multilocus perspectives on the impact of changes in climate and sea level on the population history of widespread species with disjunct ranges in Australia and New Guinea.     

Isolation‐driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae)

Lineage, or true ‘species’, trees may differ from gene trees because of stochastic processes in molecular evolution leading to gene‐tree heterogeneity. Problems with inferring species trees because of excessive incomplete lineage sorting may be exacerbated in lineages with rapid diversification or recent divergences necessitating the use of multiple loci and individuals. Many recent multilocus studies that investigate divergence times identify lineage splitting to be more recent than single‐locus studies, forcing the revision of biogeographic scenarios driving divergence. Here, we use 21 nuclear loci from regional populations to re‐evaluate hypotheses identified in an mtDNA phylogeographic study of the Brown Creeper (Certhia americana), as well as identify processes driving divergence. Nuclear phylogeographic analyses identified hierarchical genetic structure, supporting a basal split at approximately 32°N latitude, splitting northern and southern populations, with mixed patterns of genealogical concordance and discordance between data sets within the major lineages. Coalescent‐based analyses identify isolation, with little to no gene flow, as the primary driver of divergence between lineages. Recent isolation appears to have caused genetic bottlenecks in populations in the Sierra Madre Oriental and coastal mountain ranges of California, which may be targets for conservation concerns.     

GEOGRAPHIC DISTRIBUTION OF MITOCHONDRIAL DNA VARIANTS AND THE HISTORICAL BIOGEOGRAPHY OF THE SPOTTED SALAMANDER,AMBYSTOMA MACULATUM

I analyzed geographic partitioning of mitochondrial DNA (mtDNA) restriction-site variants in the spotted salamander, Ambystoma maculatum. Two highly divergent and geographically separate genetic lineages were identified that differed by a minimum of 19 restriction sites (6% sequence divergence). One of the lineages has a disjunct distribution with very closely related haplotypes occurring in Missouri, Arkansas, North Carolina, and Virginia. The other lineage is found in Michigan, Illinois, and Alabama. The geographic separation of highly divergent mtDNA haplotypes, a pattern that was predicted based on the sedentary nature of these salamanders, is evidence for long-term barriers to gene flow. In contrast, the large-scale disjunction of very similar haplotypes suggests recent, long-distance gene flow and does not match the phylogeographic expectation for a small terrestrial vertebrate. I explain this potential contradiction in the level of importance assigned to gene flow by a scenario in which historical barriers to gene flow account for the two divergent mtDNA assemblages, but stochastic sorting of ancestral polymorphism is responsible for the large-scale geographic disjunction. Ten of 16 populations collected in the Ozark Highlands were fixed for the same haplotype. I attribute this lack of detectable variation to recent colonization of this area, a hypothesis that is supported by paleoecological data and demonstrates the potential benefits of combining data from paleobotany, geology, and other disciplines to reconstruct the historical biogeography of a species.     

Mitochondrial diversity of Opsariichthys bidens (Teleostei, Cyprinidae) in three Chinese drainages

We describe the phylogeographic structure of 28 Chinese populations of the cyprinid Opsariichthys bidens across three main Chinese river drainages. Our study is based on the phylogenetic analysis of the complete mitochondrial cytochrome b gene (1140 bp). We combined this analysis with population processes inferred from nested clade analysis (NCA) and mismatch distributions. Both analyses showed that Chinese O. bidens consists of five mtDNA lineages (Opsariichthys 1-5) with high genetic divergence among them. Molecular divergences (TrN+G) higher than 20% among the Opsariichthys 1-5 mtDNA lineages suggest a taxonomic underestimation at the species level. About 92% of the genetic variance among samples was explained by differences among Opsariichthys mtDNA lineages. Drainage-restricted haplotypes with high frequencies and moderate nucleotide diversity show that Opsariichthys populations have evolved independently. NCA results were congruent with the phylogeny, and unimodal mismatch distributions with negative Tajima's D values suggest population expansions in some Opsariichthys lineages. The phylogeographic structure of the Opsariichthys 1-5 mtDNA lineages appears to be related to their long-term interruption of gene flow (theta(ST)>0.97). Our results suggested that fragmentation of ancestral ranges might have caused Opsariichthys diversification in Chinese waters. However, current distribution of common haplotypes across the Yangtze and Pearl drainages suggests a recent river connection that could have favoured gene flow across drainages. Overall, the results indicated that the richness of current Asian widespread species might have been underestimated, and that the cyprinid populations of O. bidens in the Yangtze, Pearl and Hai He drainages may correspond to five species.     

Phylogeography of the planktonic chaetognath Sagitta setosa reveals isolation in European seas

Numerous planktonic species have disjunct distribution patterns in the world's oceans. However, it is unclear whether these are truly unconnected by gene flow, or whether they are composed of morphologically cryptic species. The marine planktonic chaetognath Sagitta setosa Müller has a discontinuous geographic distribution over the continental shelf in the northeastern Atlantic, Mediterranean Sea, and Black Sea. Morphological variation between these populations has been described, but overlaps and is therefore unsuitable to determine the degree of isolation between populations. To test whether disjunct populations are also genetically disjunct, we sequenced a 504-bp fragment of mitochondrial DNA comprising the cytochrome oxidase II region of 86 individuals. Sequences were highly variable; each represented a different haplotype. Within S. setosa, sequence divergence ranged from 0.2 to 8.1% and strong phylogeographic structure was found, with four main groups corresponding to the northeastern Atlantic, Mediterranean Sea (including Ligurian Sea, Tyrrhenian Sea and Gulf of Gabes), Adriatic Sea, and Black Sea. Two of these (Atlantic and Black Sea) were resolved as monophyletic clades, thus gene flow between disjunct populations of S. setosa has been extremely limited and lineage sorting has taken place. The deepest divergence was between Atlantic and Mediterranean/Black Sea populations followed by a split between Mediterranean and Black Sea populations. The Mediterranean/Black Sea clade comprised three groups, with the Adriatic Sea as the most likely sister clade of the Black Sea. These data are consistent with a colonization of the Black Sea from the Mediterranean. Furthermore, a possible cryptic species was found in the Black Sea with 23.1% sequence divergence from S. setosa. Two possibilities for the evolutionary origin of this species are proposed, namely, that it represents a relict species from the ancient Paratethys, or that it represents another chaetognath species that colonized the Black Sea more recently. Even though the exact timing of disjunction of S. setosa populations remains unclear, on the basis of the geological and paleoclimatic history of the European basins and our estimates of net nucleotide divergence, we suggest that disjunct populations arose through vicariance resulting from the cyclical changes in temperature and sea levels during the Pleistocene. We conclude that these populations have remained disjunct, not because of limited dispersal ability, but because of the inability to maintain viable populations in suboptimal, geographically intermediate areas.     

Parallel evolution and vicariance in the guppy (Poecilia reticulata) over multiple spatial and temporal scales

Well-studied model systems present ideal opportunities to understand the relative roles of contemporary selection versus historical processes in determining population differentiation and speciation. Although guppy populations in Trinidad have been a model for studies of evolutionary ecology and sexual selection for more than 50 years, this work has been conducted with little understanding of the phylogenetic history of this species. We used variation in nuclear (X-src) and mitochondrial DNA (mtDNA) sequences to examine the phylogeographic history of Poecilia reticulata Peters (the guppy) across its entire natural range, and to test whether patterns of morphological divergence are a consequence of parallel evolution. Phylogenetic, nested clade, population genetic, and demographic analyses were conducted to investigate patterns of genetic structure at several temporal scales and are discussed in relation to vicariant events, such as tectonic activity and glacial cycles, shaping northeast South American river drainages. The mtDNA phylogeny defined five major lineages, each associated with one or more river drainages, and analysis of molecular variance also detected geographic structuring among these river drainages in an evolutionarily conserved nuclear (X-src) locus. Nested clade and other demographic analyses suggest that the eastern Venezuela/ western Trinidad region is likely the center of origin of P. reticulata. Mantel tests show that the divergence of morphological characters, known to differentiate on a local scale in response to natural and sexual selection pressures, is not associated with mtDNA genetic distance; however, TreeScan analysis identified several significant associations of these characters with the haplotype tree. Parallel upstream/downstream patterns of morphological adaptation in response to selection pressures reported in P. reticulata within Trinidad rivers appears to persist across the natural range. Our results together with previous studies suggest that, although morphological variation in P. reticulata is primarily attributed to selection, phylogeographic history may also play a role.     

GLOBAL MITOCHONDRIAL DNA PHYLOGEOGRAPHY OF HOLARCTIC BREEDING DUNLINS (CALIDRIS ALPINA)

Comparison of mitochondrial DNA (mtDNA) control-region sequences of 155 dunlins from 15 breeding populations confirmed the existence of five major phylogeographic groups in the circumpolar breeding range of this migratory shorebird species. Time estimates of the origin of groups, based on sequence divergences and a molecular clock for birds, suggest a scenario of repeated fragmentation of populations in isolated tundra refugia during the late Pleistocene. The distribution of about three-quarters of all detected molecular variance between phylogeographic groups attests to the strongly subdivided genetic population structure in dunlins that is being maintained by natal philopatry. Each mtDNA phylogeographic group can be related to a morphometrically defined subspecies, but several other recognized subspecies are not supported by monophyletic mtDNA lineages within their purported ranges. More detailed analysis of several European populations reveals low amounts of gene flow and the partitioning of a substantial fraction of molecular variance between them. This ongoing evolution of population-genetic structuring within the European phylogeographic group most likely started with the last retreat of the ice sheets some 10,000 years ago. Dunlins thus provide one of the clearest examples of the linkage between historical and contemporary components of mtDNA phylogeographic structuring in birds.     

Mitochondrial DNA Sequence Variation of the Swallowtail Butterfly, Papilio xuthus, and the Cabbage Butterfly, Pieris rapae

We analyzed a portion of mitochondrial COI gene sequences (658 bp) to investigate the genetic diversity and geographic variation of the swallowtail butterfly, Papilio xuthus L. (Lepidoptera: Papilionidae), and the cabbage butterfly, Pieris rapae L. (Lepidoptera: Pieridae). Papilio xuthus showed a moderate level of sequence divergence (0.91% at maximum) in 15 haplotypes, whereas Pi. rapae showed a moderate to high level of sequence divergence (1.67% at maximum) in 30 haplotypes, compared with other relevant studies. Analyses of population genetic structure showed that most populations are not genetically differentiated in both species. The distribution pattern of both species appears to be consistent with category IV of the phylogeographic pattern sensu Avise: a phylogenetic continuity, an absence of regional isolation of mtDNA clones, and extensive distribution of close clones. The observed pattern of genetic diversity and geographic variation of the two butterfly species seem to reflect the abundant habitats, abundant host plants, and flying abilities in connection with the lack of historical biogeographic barriers.     

Connecting the dots: Bridging genetic and spatial differentiation of the genus Eumerus (Diptera: Syrphidae) in the Mediterranean Basin and Balkans

In this study, we explored intraspecific genetic differentiation of hoverfly species of the genus Eumerus with regard to landscape discontinuities (due to paleogeological events), isolation‐by‐distance, evolutionary processes, and Quaternary climatic oscillations. We unveil genetically diverging regions and discuss the potential driving forces that gave rise to these spatial genetic patterns. We generated mitochondrial DNA (mtDNA) barcodes for 274 individuals of nine Eumerus species, sampled from 58 localities in the Mediterranean and Balkans. Spatially explicit Bayesian clustering, correlation tests between geographic and genetic distances (presence of isolation‐by‐distance), median neighbor‐joining haplotype networks, and landscape shape interpolation analyses were employed to investigate spatial genetic patterns. Bayesian clustering generated one to three genetic clusters with high posterior probability values. We also observed high mtDNA haplotype diversity consisting of unique and shared haplotypes, as well as starlike mtDNA haplotype patterns. The mtDNA haplotype network was consistent with species distributions and Bayesian clustering for four tested species. The Mantel tests confirmed the absence of isolation‐by‐distance in seven species. We identified genetically diverging areas through our landscape shape interpolation analyses. Five species displayed neither spatial genetic patterns nor evidence of isolation‐by‐distance, indicative of relict taxa. Our study is the first broad‐ and large‐scale study of Eumerus species in the Mediterranean and Balkans; it reveals spatial genetic clusters in four species and identifies the potential factors driving those patterns.     

用ISSR标记分析不同地区紫茎泽兰种群的遗传变异

利用ISSR标记技术分析了我国32个紫茎泽兰地理种群的遗传多样性,结果表明入侵我国的紫茎泽兰具有较大的遗传多样性,物种水平上的Nei's基因多样性为0．235,shannon's指数为0．372。种群间的遗传分化研究表明,大部分变异存在于种群内,总体遗传多样性中仅34．5%来源于种群之间。紫茎泽兰种群间的遗传距离矩阵和空间距离矩阵之间呈轻度正相关(r=0．542,P＜0．001),说明地理隔离可能是阻碍紫茎泽兰种群间基因交流的原因之一。不同海拔高度紫茎泽兰种群的遗传多样性水平呈现随海拔升高而降低的趋势(r=0．368,P＜0．001),各海拔区域种群的平均ISSR标记Nei's基因多样性和Shannon's指数均随海拔升高而有所降低。     

Phylogeography and the origins of range disjunctions in a north temperate fish,the pygmy whitefish (Prosopium coulterii), inferred from mitochondrial and nuclear DNA sequence analysis

Aim To investigate the degree of phylogeographical divergence within pygmy whitefish (Prosopium coulterii) and to test hypotheses concerning the origin of disjunct populations within North America. Location North America from western Alaska to Lake Superior. Methods Mitochondrial (ATPase subunit VI) and nuclear (ITS‐1, ITS‐2) DNA sequence variation was assessed across the species’ North American range to test for the existence of distinct phylogeographical groupings of pygmy whitefish associated with known glacial refugia. Coalescent simulations of the mitochondrial DNA (mtDNA) data were used to test hypotheses of population structure. Results This species is composed of two monophyletic mitochondrial clades across its North American range. The two mtDNA clades differed by an average 3.3% nucleotide sequence divergence. These clades were also distinguished by ITS‐2, but the relationships among lineages were not resolved by the ITS‐1 analysis. Coalescent analyses rejected the null hypothesis of the current disjunct distributions being a result of fragmentation of a single widespread ancestral lineage across a variety of effective population sizes and divergence times. Main conclusions The current range disjunctions of pygmy whitefish in North America probably resulted from isolation, genetic divergence, and selective dispersal from at least two major Pleistocene glacial refugia: Beringia and Cascadia. More recent isolation and dispersal from an upper Mississippi refugium is suggested by relationships within one of the clades and by distributional evidence from co‐distributed species. The Beringian and Cascadian refugia have played major roles in the zoogeography of Nearctic temperate aquatics, but the roles of smaller refugia appear more variable among other species.     

Phylogeographic analyses of the southern leopard frog: the impact of geography and climate on the distribution of genetic lineages vs. subspecies

The southeastern United States is a major phylogeographic break hotspot for amphibians, but the processes underlying this hotspot remain to be explicitly tested. We test the correlation of genetic lineages with subspecies breaks in the southeastern United States and the association of such breaks with climate, using Rana sphenocephala as a case study, and place our results in the broader context of the Alabama‐Appalachian suture zone (AL‐Appalachian SZ). We use genetic and ecological methods to (i) determine whether genetic lineages are coincident with the AL‐Appalachian SZ or the subspecies and (ii) test the correlation of major climatic breaks with genetic structure and morphological variation in R. sphenocephala. Bayesian phylogenetic analyses of the ND1 mtDNA gene and microsatellite cluster analyses revealed two distinct lineages with over 4% sequence divergence. The geographic distributions of the two lineages are concordant with the AL‐Appalachian SZ but do not correspond to the ranges of the subspecies based on morphology. Mantel tests revealed that isolation by distance and historical barriers to gene flow, rather than climate, are the major drivers of genetic divergence at neutral loci. Examination of climate breaks across the Southeast revealed a pattern incongruent with suture zone hotspots, suggesting that phylogenetic structure has been driven primarily by historical factors, such as isolation, the Appalachian Mountains and the Apalachicola/Chattahoochee/Flint River Basin. However, climate breaks are consistent with the geographic distribution of the subspecies of R. sphenocephala, suggesting that environmental pressures may be driving divergence in morphological traits that outpaces molecular evolution.     

The geographic structure of morphological variation in eight species of fiddler crabs (Ocypodidae: genus Uca) from the eastern United States and Mexico

Species with larger geographic distributions are more likely to encounter a greater variety of environmental conditions and barriers to gene flow than geographically‐restricted species. Thus, even closely‐related species with similar life‐history strategies might vary in degree and geographic structure of variation if they differ in geographic range size. In the present study, we investigated this using samples collected across the geographic ranges of eight species of fiddler crabs (Crustacea: Uca) from the Atlantic and Gulf coasts of North America. Morphological variation in the carapace was assessed using geometric morphometric analysis of 945 specimens. Although the eight Uca species exhibit different degrees of intraspecific variation, widespread species do not necessarily exhibit more intraspecific or geographic variation in carapace morphology. Instead, species with more intraspecific variation show stronger morphological divergence among populations. This morphological divergence is partly a result of allometric growth coupled with differences in maximum body size among populations. On average, 10% of total within‐species variation is attributable to allometry. Possible drivers of the remaining morphological differences among populations include gene flow mediated by ocean currents and plastic responses to various environmental stimuli, with isolation‐by‐distance playing a less important role. The results obtained indicate that morphological divergence among populations can occur over shorter distances than expected based on dispersal potential. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 248–270.     

Hidden phylogeographic complexity in the Sierra Madre Oriental: the case of the Mexican tulip poppy Hunnemannia fumariifolia (Papaveraceae)

Aim A phylogeographic study of the endemic Mexican tulip poppy Hunnemannia fumariifolia (Papaveraceae) was conducted to determine: (1) the historical processes that influenced its geographical pattern of genetic variation; (2) whether isolation by distance was one of the main factors that caused genetic divergence in populations of this species; and (3) whether genetic flow still exists between populations from northern arid zones (Chihuahuan Desert and Sierra Madre Oriental) and those from southern arid zones (Tehuacán‐Cuicatlán Valley) – populations that are separated by the Transvolcanic Belt. Location Xerophytic vegetation in Mexico. Methods Chloroplast DNA (cpDNA) sequences of three regions, trnH‐psbA, rpl32‐trnL(UAG) and ndhF‐rpl32, were obtained for 85 individuals from 17 populations sampled in the field, covering the entire range of H. fumariifolia. The evolutionary history of these populations was investigated using a nested clade phylogeographic analysis and also by conducting various population genetic analyses. Results In total, 17 haplotypes were detected, 14 of which were found in the Sierra Madre Oriental. Differentiation among populations based on cpDNA variation (G_ST = 0.787, SE 0.0614) indicated population structure in H. fumariifolia, corroborated by a fixation index (F_ST) of 0.907. Results from analysis of molecular variance found that most of the total variation (90.71%, P < 0.001) was explained by differences among populations. Three regions were determined based on geological correspondence – the Chihuahuan Desert, Sierra Madre Oriental and Tehuacán‐Cuicatlán Valley – and the variation between them was significant (43.39%, P < 0.001). Results of a Mantel test showed a significant correlation between genetic and geographic distances (r = 0.511; P = 0.0001), suggesting a pattern of isolation by distance, which was corroborated by nested clade phylogeographic analysis. Mismatch distribution analysis indicated a sudden demographic expansion. Main conclusions Our study found that isolation by distance influenced genetic divergence in populations of H. fumariifolia. The finding that allopatric fragmentation influenced genetic divergence in populations in the Sierra Madre Oriental may be a reflection of the complex geology of the area. Our results suggest that the areas located in the north of the Sierra Madre Oriental acted as post‐glacial refugia for some populations.     

Effects of the Tanaka Line on the genetic structure of Bombax ceiba (Malvaceae) in dry‐hot valley areas of southwest China

Southwest China is an important biodiversity hotspot. The interactions among the complex topography, climate change, and ecological factors in the dry‐hot valley areas in southwest China may have profoundly affected the genetic structure of plant species in this region. In this study, we determined the effects of the Tanaka Line on genetic variation in the wild Bombax ceiba tree in southwest China. We sampled 224 individuals from 17 populations throughout the dry‐hot valley regions. Six polymorphic expressed sequence tag–simple sequence repeat primers were employed to sequence the PCR products using the first‐generation Sanger technique. The analysis based on population genetics suggested that B. ceiba exhibited a high level of gene diversity (H_E: 0.2377–0.4775; I: 0.3997–0.7848). The 17 populations were divided into two groups by cluster analysis, which corresponded to geographic characters on each side of the Tanaka Line. In addition, a Mantel test indicated that the phylogeographic structure among the populations could be fitted to the isolation‐by‐distance model (r² = .2553, p < .001). A barrier test indicated that there were obstacles among populations and between the two groups due to complex terrain isolation and geographic heterogeneity. We inferred that the Tanaka Line might have promoted the intraspecific phylogeographic subdivision and divergence of B. ceiba. These results provide new insights into the effects of the Tanaka Line on genetic isolation and population differentiation of plant species in southwest China.     

Application of a Random Walk Model to Geographic Distributions of Animal Mitochondrial DNA Variation

In rapidly evolving molecules, such as animal mitochondrial DNA, mutations that delineate specific lineages may not be dispersed at sufficient rates to attain an equilibrium between genetic drift and gene flow. Here we predict conditions that lead to nonequilibrium geographic distributions of mtDNA lineages, test the robustness of these predictions and examine mtDNA data sets for consistency with our model. Under a simple isolation by distance model, the variance of an mtDNA lineage's geographic distribution is expected be proportional to its age. Simulation results indicated that this relationship is fairly robust. Analysis of mtDNA data from natural populations revealed three qualitative distributional patterns: (1) significant departure of lineage structure from equilibrium geographic distributions, a pattern exhibited in three rodent species with limited dispersal; (2) nonsignificant departure from equilibrium expectations, exhibited by two avian and two marine fish species with potentials for relatively long-distance dispersal; and (3) a progression from nonequilibrium distributions for younger lineages to equilibrium distributions for older lineages, a condition displayed by one surveyed avian species. These results demonstrate the advantages of considering mutation and genealogy in the interpretation of mtDNA geographic variation.     

PHYLOGEOGRAPHY OF THE JUMPING SPIDER HABRONATTUS PUGILLIS (ARANEAE: SALTICIDAE): RECENT VICARIANCE OF SKY ISLAND POPULATIONS?

In island systems with diverging populations, the history of island formation and genealogical estimates of divergence dates can be mutually informative. In the "sky islands" of southeastern Arizona, climate-induced contraction of woodlands appears to have fragmented populations of woodland-dwelling species onto disjunct mountain ranges. Montane populations of the jumping spider, Habronattus pugillis, display striking amounts of phenotypic divergence among ranges. Paleoclimatic estimates date woodland fragmentation at approximately 10,000 years ago, suggesting that phenotypic divergence has been extraordinarily rapid in these spiders. This phylogeographic study of populations of H. pugillis attempts to clarify the species' history of isolation and divergence and to address the suitability of available paleoclimatic data for dating divergences among populations of the region's woodland-dwelling organisms. Mitochondrial sequence data of spiders from 13 mountain ranges was used to reconstruct genealogical relationships. Gene trees show that small mountain ranges tend to have populations whose sequences form monophyletic groups, whereas larger ranges do not. Paraphyly among genes from larger ranges could result from either recent migration or incomplete lineage sorting. I use phylogenetic and geographic information to test these alternatives, and conclude that incomplete lineage sorting best explains the observed paraphyly. Gene trees are concordant with some of the predictions of vegetation history generated by examination of topography. Dates estimated for divergence of populations vary from 30,000 years to more than 2 million years ago, suggesting multiple vicariance events that are older than would be inferred from paleoclimatic studies. These findings illustrate that use of any single paleontological dataset to calibrate molecular clocks can potentially greatly underestimate actual divergence times.     

PERCHED AT THE MITO‐NUCLEAR CROSSROADS: DIVERGENT MITOCHONDRIAL LINEAGES CORRELATE WITH ENVIRONMENT IN THE FACE OF ONGOING NUCLEAR GENE FLOW IN AN AUSTRALIAN BIRD

Relationships among multilocus genetic variation, geography, and environment can reveal how evolutionary processes affect genomes. We examined the evolution of an Australian bird, the eastern yellow robin Eopsaltria australis, using mitochondrial (mtDNA) and nuclear (nDNA) genetic markers, and bioclimatic variables. In southeastern Australia, two divergent mtDNA lineages occur east and west of the Great Dividing Range, perpendicular to latitudinal nDNA structure. We evaluated alternative scenarios to explain this striking discordance in landscape genetic patterning. Stochastic mtDNA lineage sorting can be rejected because the mtDNA lineages are essentially distinct geographically for > 1500 km. Vicariance is unlikely: the Great Dividing Range is neither a current barrier nor was it at the Last Glacial Maximum according to species distribution modeling; nuclear gene flow inferred from coalescent analysis affirms this. Female philopatry contradicts known female‐biased dispersal. Contrasting mtDNA and nDNA demographies indicate their evolutionary histories are decoupled. Distance‐based redundancy analysis, in which environmental temperatures explain mtDNA variance above that explained by geographic position and isolation‐by‐distance, favors a nonneutral explanation for mitochondrial phylogeographic patterning. Thus, observed mito‐nuclear discordance accords with environmental selection on a female‐linked trait, such as mtDNA, mtDNA–nDNA interactions or genes on W‐chromosome, driving mitochondrial divergence in the presence of nuclear gene flow.     

Hard and soft allopatry: physically and ecologically mediated modes of geographic speciation

Aim Three common patterns have emerged in comparative phylogeographic analyses at many barriers: (1) a potential geographic pseudocongruence of lineage divergences; (2) a disconnect between the inference of temporally clustered, relatively recent timing for observed speciation events, and dates spanning a broader, apparently random time‐scale; and (3) an apparent prevalence of speciation with recent or continuing gene flow. It is unclear if there is a unifying explanation for these phenomena. We argue that the interaction between geographic barriers to dispersal and ecological limits on the distribution of species can explain these patterns. We suggest that these patterns can be explained by the presence of a continuum between two underlying processes, here termed ‘hard’ and ‘soft’ allopatric divergence, which result from the interplay between organismal ecology and the physioecological nature of geographic barriers. Location Examples from North America. Methods We examine comparative phylogeographic divergences in 18 groups of terrestrial vertebrates at two major biogeographic features in North America – the Mississippi River Embayment and the Cochise Filter Barrier – to test predictions made by this hypothesis. Results We find support for the two distinct processes of hard and soft allopatry, and note several examples exhibiting characteristics of both. Hard allopatry is caused by physical barriers promoting divergence as a function of consistent geographic isolation. Soft allopatry is caused by ecological processes that isolate populations geographically in allopatric refugia through niche conservatism, or across ecological transition zones through niche divergence, but which may be periodic or inconsistent through time. Main conclusions Viewing geographic speciation as a continuum between hard and soft allopatry can explain all three patterns as a consequence of the physical and ecological mechanisms that isolate populations, and provides an alternative perspective on the impact of ecological factors and physical barriers on lineage formation.     

Deep sympatric mitochondrial divergence without reproductive isolation in the common redstart Phoenicurus phoenicurus

Mitochondrial DNA usually shows low sequence variation within and high sequence divergence among species, which makes it a useful marker for phylogenetic inference and DNA barcoding. A previous study on the common redstart (Phoenicurus phoenicurus) revealed two very different mtDNA haplogroups (5% K2P distance). This divergence is comparable to that among many sister species; however, both haplogroups coexist and interbreed in Europe today. Herein, we describe the phylogeographic pattern of these lineages and test hypotheses for how such high diversity in mtDNA has evolved. We found no evidence for mitochondrial pseudogenes confirming that both haplotypes are of mitochondrial origin. When testing for possible reproductive barriers, we found no evidence for lineage‐specific assortative mating and no difference in sperm morphology, indicating that they are not examples of cryptic species, nor likely to reflect the early stages of speciation. A gene tree based on a short fragment of cytochrome c oxidase subunit 1 from the common redstart and 10 other Phoenicurus species, showed no introgression from any of the extant congenerics. However, introgression from an extinct congeneric cannot be excluded. Sequences from two nuclear introns did not show a similar differentiation into two distinct groups. Mismatch distributions indicated that the lineages have undergone similar demographic changes. Taken together, these results confirm that deeply divergent mitochondrial lineages can coexist in biological species. Sympatric mtDNA divergences are relatively rare in birds, but the fact that they occur argues against the use of threshold mtDNA divergences in species delineation.