Patterns of niche filling and expansion across the invaded ranges of an Australian lizard

Studies of realized niche shifts in alien species typically ignore the potential effects of intraspecific niche variation and different invaded‐range environments on niche lability. We incorporate our detailed knowledge of the native‐range source populations and global introduction history of the delicate skink Lampropholis delicata to examine intraspecific variation in realized niche expansion and unfilling, and investigate how alternative niche modelling approaches are affected by that variation. We analyzed the realized niche dynamics of L. delicata using an ordination method, ecological niche models (ENMs), and occurrence records from 1) Australia (native range), 2) New Zealand, 3) Hawaii, 4) the two distinct native‐range clades that were the sources for the New Zealand and Hawaii introductions, and 5) the species’ global range (including Lord Howe Island, Australia). We found a gradient of realized niche change across the invaded ranges of L. delicata: niche stasis on Lord Howe Island, niche unfilling in New Zealand (16%), and niche unfilling (87%) and expansion (14%) in Hawaii. ENMs fitted to native‐range data generally identified suitable climatic conditions at sites where the species has established non‐native populations, whereas ENMs based on native‐range source clades and non‐native populations had lower spatial transferability. Our results suggest that the extent to which realized niches are maintained during invasion does not depend on species‐level traits. When realized niche shifts are predominately due to niche unfilling, fully capturing species’ responses along climatic gradients by basing ENMs on native distributions may be more important for accurate invasion forecasts than incorporating phylogenetic differentiation, or integrating niche changes in the invaded range.     

Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range‐wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil‐calibrated and rate‐calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide‐ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well‐supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co‐distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid‐adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 949–967.     

Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida,Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis‐based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane‐restricted cryophilic harvestman, Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double‐digest RAD‐seq data and conducted population‐level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid‐latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of S. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre‐dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model‐based coalescent approaches, we find support for postdivergence migration between clades from separate refugia.     

Population structure and biogeography of Hemiphaga pigeons (Aves: Columbidae) on islands in the New Zealand region

Aim The New Zealand avifauna includes lineages that lack close relatives elsewhere and have low diversity, characteristics sometimes ascribed to long geographic isolation. However, extinction at the population and species levels could yield the same pattern. A prominent example is the ecologically important pigeon genus Hemiphaga. In this study, we examined the population structure and phylogeography of Hemiphaga across islands in the region. Location New Zealand, Chatham Islands and Norfolk Island. Methods Mitochondrial DNA was sequenced for all species of the genus Hemiphaga. Sixty‐seven individuals from mainland New Zealand (Hemiphaga novaeseelandiae novaeseelandiae), six of the Chatham Islands sister species (Hemiphaga chathamensis), and three of the extinct Norfolk Island subspecies (Hemiphaga novaeseelandiae spadicea) were included in this study. Novel D‐loop and cytochrome b primers were designed to amplify DNA from museum samples. Additionally, five other mitochondrial genes were used to examine placement of the phylogenetic root. Results Analyses of mitochondrial DNA sequences revealed three Hemiphaga clades, consistent with the allopatric populations of recognized (sub)species on oceanic islands. Of the 23 D‐loop haplotypes among 67 New Zealand pigeons (Hemiphaga n. novaeseelandiae), 19 haplotypes were singletons and one haplotype was common and widespread. Population genetic diversity was shallow within and between New Zealand populations, indicating range expansion with high inter‐population exchange. Tentative rooting of the Hemiphaga clade with cyt b data indicates exchange between mainland New Zealand and the Chatham Islands prior to colonization of Norfolk Island. We found low genetic divergence between populations on New Zealand, the Chatham Islands and Norfolk Island, but deep phylogenetic divergence from the closest living relatives of Hemiphaga. Main conclusions The data are consistent with the hypothesis of population reduction during the Pleistocene and subsequent expansion from forest refugia. Observed mobility of Hemiphaga when feeding helps explain the shallow diversity among populations on islands separated by many hundreds of kilometres of ocean. Together with comparison of distribution patterns observed among birds of the New Zealand region, these data suggest that endemicity might represent not long occupancy of an area, but descent from geologically recent colonizations. We consider the role of lineage pruning in creating the impression of old endemicity.     

Historical biogeography of two alpine butterflies in the Rocky Mountains: broad-scale concordance and local-scale discordance

Aim We inferred the phylogeography of the alpine butterfly Colias meadii Edwards (Pieridae) and compared its genetic structure with that of another high elevation, co‐distributed butterfly, Parnassius smintheus Doubleday (Papilionidae), to test if the two Rocky Mountain butterflies responded similarly to the palaeoclimatic cycles of the Quaternary. Location Specimens were collected from 18 alpine sites in the Rocky Mountains of North America, from southern Colorado to northern Montana. Methods We sequenced 867 and 789 nucleotides of cytochrome oxidase I from an average of 19 and 20 individuals for C. meadii and P. smintheus, respectively, from each of the same 18 localities. From the sequence data, we calculated measures of genetic diversity within each population (H, θ), genetic divergence among populations (F_ST), and tested for geographic structure through an analysis of molecular variance (amova ). Population estimates were compared against latitude and between species using a variety of statistical tests. Furthermore, nested clade analysis was implemented to infer historic events underlying the geographic distribution of genetic variation in each species. Then, we compared the number of inferred population events between species using a nonparametric Spearman's rank correlation test. Finally, we ran coalescent simulations on each species’ genealogy to test whether the two species of Lepidoptera fit the same model of population divergence. Results Our analyses revealed that: (1) measures of within‐population diversity were not correlated with latitude for either species, (2) within‐site diversity was not correlated between species, (3) within a species, nearly all populations were genetically isolated, (4) both species exhibited significant and nearly identical partitioning of genetic variation at all hierarchical levels of the amova , including a strong break between populations across the Wyoming Basin, (5) both species experienced similar cycles of expansion and contraction, although fewer were inferred for C. meadii, and (6) data from both species fit a model of three refugia diverging during the Pleistocene. Main conclusions While our findings supported a shared response of the two butterfly species to historic climate change across coarse spatial scales, a common pattern was not evident at finer spatial and temporal scales. The shared demographic history of the two species is consistent with an expanding–contracting archipelago model, suggesting that populations persisted across the geographic range throughout the climate cycles, experiencing isolation on ‘sky islands’ during interglacial periods and becoming connected as they migrated down‐slope during cool, wet climates.     

The role of topography in structuring the demographic history of the pine processionary moth,Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

Aim We investigated the Quaternary history of the pine processionary moth, Thaumetopoea pityocampa, an oligophagous insect currently expanding its range. We tested the potential role played by mountain ranges during the post‐glacial recolonization of western Europe. Location Western Europe, with a focus on the Pyrenees, Massif Central and western Alps. Methods Maternal genetic structure was investigated using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. We analysed 412 individuals from 61 locations and performed maximum likelihood and maximum parsimony phylogenetic analyses and hierarchical analysis of molecular variance, and we investigated signs of past expansion. Results A strong phylogeographic pattern was found, with two deeply divergent clades. Surprisingly, these clades were not separated by the Pyrenees but rather were distributed from western to central Iberia and from eastern Iberia to the Italian Peninsula, respectively. This latter group consisted of three shallowly divergent lineages that exhibited strong geographic structure and independent population expansions. The three identified lineages occurred: (1) on both sides of the Pyrenean range, with more genetically diverse populations in the east, (2) from eastern Iberia to western France, with a higher genetic diversity in the south, and (3) from the western Massif Central to Italy. Admixture areas were found at the foot of the Pyrenees and Massif Central. Main conclusions The identified genetic lineages were geographically structured, but surprisingly the unsuitable high‐elevation areas of the main mountainous ranges were not responsible for the spatial separation of genetic groups. Rather than acting as barriers to dispersal, mountains appear to have served as refugia during the Pleistocene glaciations, and current distributions largely reflect expansion from these bottlenecked refugial populations. The western and central Iberian clade did not contribute to the northward post‐glacial recolonization of Europe, yet its northern limit does not correspond to the Pyrenees. The different contributions of the identified refugia to post‐glacial expansion might be explained by differences in host plant species richness. For example, the Pyrenean lineage could have been trapped elevationally by tracking montane pines, while the eastern Iberian lineage could have expanded latitudinally by tracking thermophilic lowland pine species.     

Pleistocene climate changes shaped the divergence and demography of Asian populations of the great tit Parus major: evidence from phylogeographic analysis and ecological niche models

Different scales and frequencies of glaciations developed in Europe and Asia during the Pleistocene. Because species’ responses to climate change are influenced by interactive factors including ecology and local topography, the pattern and tempo of species diversification may vary significantly across regions. The great tit Parus major is a widespread Eurasian passerine with a range that encircles the central Asian desert and high‐altitude areas of the Tibetan Plateau. A number of genetic studies have assessed the effect of paleo‐climate changes on the distribution of the European population. However, none have comprehensively addressed how paleo‐climate change affected the distribution of the great tit in China, an apparent hotspot of P. major subspecific diversity. Here, we describe likely paleo‐climatic effects on P. major populations in China based on a combination of phylogeography and ecological niche models (ENMs). We sequenced three mitochondrial DNA markers from 28 populations (213 individuals), and downloaded 112 sequences from outside its Chinese range. As the first step in clarifying the intra‐specific relationships among haplotypes, we attempted to clarify the divergence and demography of populations in China. Phylogeographic analysis revealed that P. major is comprised of five highly divergent clades with geographic breaks corresponding to steep mountains and dry deserts. A previously undescribed monophyletic clade with high genetic diversity, stable niches and a long and independent evolutionary history was detected in the mountainous areas of southwest China. The estimated times at which these clades diverged was traced back to the Early‐Middle Pleistocene (2.19–0.61 mya). Contrary to the post‐LGM (the Last Glacial Maximum) expansion of European populations, demographic history indicates that Asian populations expanded before the LGM after which they remained relatively stable or grew slowly through the LGM. ENMs support this conclusion and predict a similar distribution in the present and the LGM. Our genetic and ecological results demonstrate that Pleistocene climate changes shaped the divergence and demography of P. major in China.     

The roles of rivers and Pleistocene refugia in shaping genetic diversity in Praomys misonnei in tropical Africa

Aim This study aims to elucidate the phylogeography of the murid rodent Praomys misonnei and to document whether or not rain forest refugia and rivers structure patterns of diversity within this species. Location Tropical Africa, from Ghana to Kenya. Methods Patterns of genetic structure and signatures of population history (cytochrome b gene) were assessed in a survey of 229 individuals from 54 localities. Using maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intra‐specific relationships and tested hypotheses for historical patterns of gene flow within P. misonnei. Results Our phylogenetic analyses reveal a strong phylogeographical structure. We identified four major geographical clades within P. misonnei: one clade in Ghana and Benin, a Nigerian clade, a West Central African clade and a Central and East African clade. Several subclades were identified within these four major clades. A signal of population expansion was detected in most clades or subclades. Coalescence within all of the major clades of P. misonnei occurred during the Middle Pleistocene and/or the beginning of Late Pleistocene. Main conclusions Our results suggest a role for both Pleistocene refugia and rivers in structuring genetic diversity in P. misonnei. This forest‐dwelling rodent may have been isolated in a number of forest fragments during arid periods and expanded its range during wetter periods. Potential forest refugia may have been localized in Benin–Ghana, south‐western Cameroon, southern Gabon, northern Gabon and eastern Democratic Republic of Congo–western Uganda. The Niger and/or the Cross Rivers, the Oubangui‐Congo, Sanaga, Ogooue and/or Ivindo Rivers probably stopped the re‐expansion of the species from relict areas.     

Origins and patterns of endemic diversity in two specialized lizard lineages from the Australian Monsoonal Tropics (Oedura spp.)

Aim

Savanna biomes cover around 20% of land surfaces, yet the origins and processes that have shaped their biodiversity remain understudied. Here, we assess the timing of diversification and how patterns of genetic diversity vary along an aridity gradient in specialized saxicoline gecko clades (Oedura spp.) from the tropical savannas of northern Australia.

Location

Australian Monsoonal Tropics (AMT), Kimberley region (Western Australia).

Methods

We compiled mitochondrial and nuclear data for two Kimberley endemic lizard clades (Oedura filicipoda/murrumanu and O. gracilis), and allied non‐Kimberley taxa (O. marmorata complex). Species delimitation methods were used to identify evolutionary lineages, Maximum‐likelihood and Bayesian phylogenetic methods were employed to assess relationships and diversification timeframes, and rainfall data and range sizes were tested for correlations.

Results

Phylogenetic analyses of cryptic or recently discovered lineage diversity revealed late‐Miocene to early‐Pliocene crown ages. Microendemism and diversity were highest in high‐rainfall regions, while the most widespread lineages occurred in the central and south‐east Kimberley, and showed evidence of introgression with parapatric lineages.

Main conclusions

The initial diversification in both clades was broadly concordant with global climatic events linked to the expansion of savanna biomes in the lateMiocene. Higher endemism in mesic and refugial areas suggests long histories of localized persistence, while wider distributions and evidence of introgression suggest a dynamic history at the arid‐monsoonal interface.     

Genomic signatures of evolution in Nautilus—An endangered living fossil

Living fossils are survivors of previously more diverse lineages that originated millions of years ago and persisted with little morphological change. Therefore, living fossils are model organisms to study both long‐term and ongoing adaptation and speciation processes. However, many aspects of living fossil evolution and their persistence in the modern world remain unclear. Here, we investigate three major aspects of the evolutionary history of living fossils: cryptic speciation, population genetics and effective population sizes, using members of the genera Nautilus and Allonautilus as classic examples of true living fossils. For this, we analysed genomewide ddRAD‐Seq data for all six currently recognized nautiloid species throughout their distribution range. Our analyses identified three major allopatric Nautilus clades: a South Pacific clade, subdivided into three subclades with no signs of admixture between them; a Coral Sea clade, consisting of two genetically distinct populations with significant admixture; and a widespread Indo‐Pacific clade, devoid of significant genetic substructure. Within these major clades, we detected five Nautilus groups, which likely correspond to five distinct species. With the exception of Nautilus macromphalus, all previously described species are at odds with genomewide data, testifying to the prevalence of cryptic species among living fossils. Detailed F_ST analyses further revealed significant genome‐wide and locus‐specific signatures of selection between species and differentiated populations, which is demonstrated here for the first time in a living fossil. Finally, approximate Bayesian computation (ABC) simulations suggest large effective population sizes, which may explain the low levels of population differentiation commonly observed in living fossils.     

Recent origin,active speciation and dispersal for the lichen genus Nephroma (Peltigerales) in Macaronesia

Aim We reconstructed the phylogeny of the lichen genus Nephroma (Peltigerales) to assess the relationships of species endemic to Macaronesia. We estimated dates of divergences to test the hypothesis that the species arose in Macaronesia (neo‐endemism) versus the oceanic archipelagos serving as refugia for formerly widespread taxa (palaeo‐endemism). Location Cosmopolitan with a special focus on the archipelagos of the Azores, Madeira and the Canary Islands. Methods DNA sequences were obtained from 18 species for three loci and analysed using maximum parsimony, maximum likelihood and Bayesian inferences. Divergence dates were estimated for the internal transcribed spacer (ITS)‐based phylogeny using a relaxed molecular clock. Reconstruction of the ancestral geographical range was conducted using the Bayesian 50% majority rule consensus tree under a parsimony method. Results The backbone phylogenetic tree was fully supported, with Nephroma plumbeum as sister to all other species. Four strongly supported clades were detected: the Nephroma helveticum, the N. bellum, the N. laevigatum and the N. parile clades. The latter two share a common ancestor and each includes a widespread Holarctic species (N. laevigatum and N. parile, respectively) and all species endemic to Macaronesia. The data suggest a neo‐endemic origin of Macaronesian taxa, a recent range expansion from Macaronesia of both widespread species, a range expansion limited to the Mediteranean Basin and south‐western Europe for another taxon, and a long dispersal event that resulted in a speciation event in the western parts of North America. Main conclusions The Macaronesian endemic species belong to two sister clades and originated from a most recent common ancestor (MRCA) shared with one widely distributed taxon, either N. parile or N. laevigatum. Estimates of the mean divergence dates suggest that the endemics originated in the archipelagos after the rise of the volcanic islands, along with the ancestor to the now widespread species, which probably expanded their range beyond Macaronesia via long‐distance dispersal. This study provides the first phylogenetic evidence of Macaronesian neo‐endemism in lichenized fungi and provides support for the hypothesis that oceanic islands may serve as a source for the colonization of continents. However, further data are needed to properly assess the alternative hypothesis, namely colonization from western North America.     

Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late‐Pleistocene demographic expansion across the Northern Hemisphere

Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.     

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians

Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human‐mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human‐mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next‐Generation Sequencing methods, using historical museum specimens and late 20th‐century samples, and retrieved partial or near‐complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene–Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai‐Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.     

A multiple‐gene phylogeny reveals polyphyly among eastern North American Aphaenogaster species (Hymenoptera: Formicidae)

Twenty‐three Aphaenogaster species (Hymenoptera: Formicidae) occur in North America. While morphology and ecology define most species, the species limits of a group in the Eastern United States are unclear. In particular, the morphological and behavioural characters of A. carolinensis, A. picea and A. rudis overlap. These observations suggest that these three species are not monophyletic. We therefore tested the monophyly of Aphaenogaster in the context of molecular phylogenetic analyses. We used DNA data from five genes: CO1, CAD, EF1αF2, long‐wavelength rhodopsin and wingless, to reconstruct phylogenies for 44 Aphaenogaster and outgroup species. In the resulting trees, reconstructed using parsimony and Bayesian inference, species boundaries associated with well‐supported monophyletic clades of individuals in most of the 23 North American Aphaenogaster collected from multiple locations. However, some clades were unresolved, and both A. picea and A. rudis were not monophyletic. Although this may indicate that clades of multiple species represent fewer but morphologically varied species, given the short branch lengths, the lack of resolution may reflect the fact that these ants have recently radiated, and a lack of gene lineage sorting explains the non‐monophyly of species. Additional biological information concerning pre‐ and postmating barriers is needed before a complete revision of species boundaries for Aphaenogaster.     

Phylogeny and taxonomy of the genus Ilyodon Eigenmann, 1907 (Teleostei: Goodeidae), based on mitochondrial and nuclear DNA sequences

Taxonomy of the live‐bearing fish of the genus Ilyodon Eigenmann, 1907 (Goodeidae), in Mexico, is controversial, with morphology and mitochondrial genetic analyses in disagreement about the number of valid species. The present study accumulated a comprehensive DNA sequences dataset of 98 individuals of all Ilyodon species and mitochondrial and nuclear loci to reconstruct the evolutionary history of the genus. Phylogenetic inference produced five clades, one with two sub‐clades, and one clade including three recognized species. Genetic distances in mitochondrial genes (cytb: 0.5%–2.1%; coxI: 0.5%–1.1% and d‐loop: 2.3%–10.2%) were relatively high among main clades, while, as expected, nuclear genes showed low variation (0.0%–0.2%), with geographic concordance and few shared haplotypes among river basins. High genetic structure was observed among clades and within basins. Our genetic analyses, applying the priority principle, suggest the recognition only of Ilyodon whitei and Ilyodon furcidens, with I. cortesae relegated to an invalid species, the populations of which belong to I. whitei.     

Mito‐nuclear phylogeography of the cyprinid fish Gymnodiptychus dybowskii in the arid Tien Shan region of Central Asia

We evaluated the phylogeography and historical demography of the cyprinid fish Gymnodiptychus dybowskii (subfamily Schizothoracinae) across three northern Qinghai‐Tibetan Plateau (QTP) river systems in the Tien Shan range: the Kaidu River, Ili River and Junggar Basin. Results from both mtDNA (16S rRNA and Cyt b) and nuDNA (RAG‐2) resolved three reciprocally monophyletic clades, one in each of the three river basins. Estimated divergence times (highest posterior density (HPD) 2.4–3.7 Mya) are consistent with the hypothesis that these three clades are products of vicariance resulting from the intensive uplift of QTP and Tien Shan, and resulting expansion of the Taklimakan and Gurbantunggut deserts. Several lines of evidence indicate dynamic demographic histories for the three clades, with late Quaternary population bottlenecks and expansions in the Kaidu and Ili rivers and, possibly, a Holocene decline in the Junggar Basin. For conservation purposes, the three clades should be treated as species or minimally, as evolutionarily significant units (ESUs). They have experienced decades of anthropogenic disturbance and preservation of the three species/ESUs will require more sustainable management of the aquatic resources.     

Latitudinal variation in suppression of flower bud formation at high temperature in four native dandelions (Taraxacum spp.) with different distributions and genetic structures in Japan

The control of the response of flowering to temperature plays a key role in successful range‐expansion of plants. A previous study showed that the suppression of flower‐bud formation at high temperature in Taraxacum officinale decreases genetically with latitude from north to south in Japan. The present study investigated whether similar trait variation occurs among populations of native Taraxacum species in Japan. Seedlings of T. albidum (a low‐ and mid‐latitude allopolyploid), T. japonicum (a mid‐latitude diploid) and T. venustum (a high‐latitude autopolyploid) were grown at three temperatures. Time to flower‐bud appearance increased with temperature in T. japonicum and T. venustum, but did not increase in T. albidum. Time to flower‐bud appearance did not differ significantly among the three species at 14°C, but it was shorter in T. albidum than in the other two species at 19°C and 24°C. The early appearance of buds of T. albidum was confirmed by another experiment in which plants of 18 populations from the three species and T. platycarpum (a mid‐latitude diploid) grown at 19°C were used. The results clearly indicate that high‐temperature suppression of flower‐bud formation was lower in low‐latitude species than in high‐latitude species. This interspecific variation is analogous to the intraspecific variation in T. officinale. Time to bud appearance of five populations in T. albidum was homogeneous within and between the populations. The results suggest that the five populations are monoclonal and lack the sensitivity of suppression of flower‐bud formation to high temperature.     

Speciation in mountain refugia: phylogeography and demographic history of the pine siskin and black‐capped siskin complex

Following Pleistocene glacial maxima, species that adapted to temperate climates in low‐latitude refugia had to modify their ranges as climate changed, expanding either latitudinally towards the poles, or altitudinally to higher elevations in mountainous regions. Within just a few thousand years, populations taking alternative routes during interglacials became isolated from each other and subjected to different selection pressures, often leading to lineage divergence and speciation. The pine siskin Spinus pinus is a common and widespread songbird showing relative phenotypic uniformity across the North American continent. One exception is the subspecies found in the highlands of northern Central America (S. p. perplexus), which shows marked differentiation in plumage color and shares some traits with the endemic and partly sympatric black‐capped siskin S. atriceps, suggesting potential introgression or even a hybrid origin of perplexus. Relationships and species limits among pinus, perplexus and atriceps have been controversial for decades. We provide new molecular evidence to help resolve the evolutionary history of the group. Phylogenetic analysis of mitochondrial DNA and nuclear intron sequences revealed three distinct lineages within the complex, corresponding to: 1) S. pinus individuals from Canada through central Mexico (S. p. pinus and S. p. macropterus), 2) individuals from the highlands of Guatemala and Chiapas (S. p. perplexus), and 3) S. atriceps. Pine siskins across North America show evidence of a recent postglacial population expansion and extremely low levels of diversity and structure. In contrast, S. p. perplexus shows evidence of demographic stasis, reflecting long‐term isolation and restricted dispersal. Marked and diagnostic genetic differences among the three lineages in mtDNA and at least one intron, suggest that a hybrid origin of S. p. perplexus is unlikely, yet some degree of introgression between S. p. perplexus and S. atriceps cannot be ruled out in localities where they occur in sympatry.     

Genetic structure of a recent climate change‐driven range extension

The life‐history strategies of some species make them strong candidates for rapid exploitation of novel habitat under new climate regimes. Some early‐responding species may be considered invasive, and negatively impact on ‘naïve’ ecosystems. The barrens‐forming sea urchin Centrostephanus rodgersii is one such species, having a high dispersal capability and a high‐latitude range margin limited only by a developmental temperature threshold. Within this species’ range in eastern Australian waters, sea temperatures have increased at greater than double the global average rate. The coinciding poleward range extension of C. rodgersii has caused major ecological changes, threatening reef biodiversity and fisheries productivity. We investigated microsatellite diversity and population structure associated with range expansion by this species. Generalized linear model analyses revealed no reduction in genetic diversity in the newly colonized region. A ‘seascape genetics’ analysis of genetic distances found no spatial genetic structure associated with the range extension. The distinctive genetic characteristic of the extension zone populations was reduced population‐specific F_ST, consistent with very rapid population expansion. Demographic and genetic simulations support our inference of high connectivity between pre‐ and post‐extension zones. Thus, the range shift appears to be a poleward extension of the highly‐connected rangewide population of C. rodgersii. This is consistent with advection of larvae by the intensified warm water East Australian current, which has also increased Tasmanian Sea temperatures above the species’ lower developmental threshold. Thus, ocean circulation changes have improved the climatic suitability of novel habitat for C. rodgersii and provided the supply of recruits necessary for colonization.     

Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong)

The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai‐Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re‐examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.