Adaptive radiation within New Zealand endemic species of the cockroach genus Celatoblatta Johns (Blattidae): a response to Plio-Pleistocene mountain building and climate change

The South Island of New Zealand offers unique opportunities to study insect evolution due to long-term physical isolation, recent alpine habitats and high levels of biotic endemism. Using DNA sequence data from cytochrome oxidase subunit 1, we investigated the phylogeographical pattern among 10 endemic cockroach species within the genus Celatoblatta Johns (Blattidae). We tested the hypothesis that an ancestral cockroach species underwent rapid speciation in response to major climatic differentiation induced by mountain building. Results suggest that speciation was a twofold process, with an interspecific radiation of Pliocene/Pleistocene age followed by intraspecific diversification during the mid Pleistocene. Average genetic distance (maximum likelihood GTR + I + Gamma) was 9.17%, with a maximum of 14.5%. Data revealed eight deep well-supported branches, each with terminal clades. Six clades were differentiated according to morphological species, while the seventh was composed of three sympatric species. We consider the latter to be a phylogenetic species, possibly as a result of hybridization within a defined geographical area. This finding seriously challenges species distinctions for these three cockroach species. Correlation between genetic distances and a Climate Similarity Index (CSI) was negative, suggesting that species found in similar habitats are also genetically closely related. A Mantel test on within-clade genetic distances vs. linear geographical distance was positive, suggesting allopatric isolation for those haplotypes. We present a model of speciation for South Island Celatoblatta.     

Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri,Ranidae)

Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.     

Molecular data and species distribution models reveal the Pleistocene history of the mayfly Ameletus inopinatus (Ephemeroptera: Siphlonuridae)1

1. We investigated the Pleistocene and Holocene history of the rare mayfly Ameletus inopinatus EATON 1887 (Ephemeroptera: Siphlonuridae) in Europe. We used A. inopinatus as a model species to explore the phylogeography of montane, cold‐tolerant aquatic insects with arctic–alpine distributions. 2. Using species distribution models, we developed hypotheses about the species demographic history in Central Europe and the recolonisation history of Fennoscandia. We tested these hypotheses using mitochondrial cytochrome oxidase I (mtCOI) sequence data and compared our genetic results with previously generated microsatellite data to explore genetic diversity distributions of A. inopinatus. 3. We observed old lineages, deep splits and almost complete lineage sorting of mtCOI sequences among mountain ranges. These results support a periglacial survival, i.e. persistence at the periphery of Pleistocene glaciers in Central Europe. 4. There was strong differentiation between the Fennoscandian and all other populations, indicating that Fennoscandia was recolonised from a refugium not accounted for in our sampling. High degrees of population genetic structure within the northern samples suggest that Fennoscandia was recolonised by more than one lineage. However, this structure was not apparent in previously published microsatellite data, consistent with secondary contact without sexual incompatibility or with sex‐biased dispersal. 5. Our demographic analyses indicate that (i) the separation of northern and Central European lineages occurred during the early Pleistocene; (ii) Central European populations have persisted independently throughout the Pleistocene and (iii) the species extended its range about 150 000 years ago.     

WHEN COLD IS BETTER: CLIMATE-DRIVEN ELEVATION SHIFTS YIELD COMPLEX PATTERNS OF DIVERSIFICATION AND DEMOGRAPHY IN AN ALPINE SPECIALIST (AMERICAN PIKA, OCHOTONA PRINCEPS)

The genetic consequences of climate-driven range fluctuation during the Pleistocene have been well studied for temperate species, but cold-adapted (e.g., alpine, arctic) species that may have responded uniquely to past climatic events have received less attention. In particular, we have no a priori expectation for long-term evolutionary consequences of elevation shifts into and out of sky islands by species adapted to alpine habitats. Here, we examined the influence of elevation shifts on genetic differentiation and historical demography in an alpine specialist, the American pika ( Ochotona princeps ). Pika populations are divided into five genetic lineages that evolved in association with separate mountain systems, rather than lineages that reflect individual sky islands. This suggests a role for glacial-period elevation shifts in promoting gene flow among high-elevation populations and maintaining regional cohesion of genetic lineages. We detected a signature of recent demographic decline in all lineages, consistent with the expectation that Holocene climate warming has driven range retraction in southern lineages, but unexpected for northern populations that presumably represent postglacial expansion. An ecological niche model of past and future pika distributions highlights the influence of climate on species range and indicates that the distribution of genetic diversity may change dramatically with continued climate warming.     

Alpine biogeography of Parnassian butterflies during Quaternary climate cycles in North America

Growth of alpine glaciers during the Pleistocene had profound effects on montane landscapes in North America and the organisms now inhabiting alpine ecosystems. Biogeography of this region has often been viewed as a system of sky islands despite the fact that species richness patterns deviate from a strict island biogeographic model. One explanation is that alpine species are not in equilibrium because of late Quaternary geographic range shifts. Genetic data can provide evidence of nonequilibrium dynamics and the distributional shifts that occur during glaciation events in alpine landscapes. Using mitochondrial and nuclear sequence data, we examine the evolutionary history of butterflies in the Parnassius phoebus complex. We test explicit, alternative models of the biogeographic history of Parnassius smintheus and Parnassius behrii , including an equilibrium island model, ancestral radiation and fragmentation, an expanding alpine archipelago and an alpine archipelago refuge model. Our results support the alpine archipelago refuge model, in which alpine butterflies undergo population contraction during glacial climates followed by population expansion during interglacial phases. While butterflies can disperse between distant mountain ranges during glacial periods, gene flow is rare. We find evidence of recent connectivity between California and Colorado, population expansion events following deglaciation ∼20 000 years B.P., and small population sizes during the last glacial period. An analysis of lineage splitting suggests that morphological differences in P. smintheus and P. behrii are the result of late Pleistocene divergence (∼48 000 years B.P.) with limited gene flow. Our results demonstrate that spatially complex and nonequilibrium population dynamics influence alpine diversity patterns.     

Mitochondrial DNA sequences support allozyme evidence for cryptic radiation of New Zealand Peripatoides (Onychophora)

A combination of single-strand conformation polymorphism analysis (SSCP) and sequencing were used to survey cytochrome oxidase I (COI) mitochondrial DNA (mtDNA) diversity among New Zealand ovoviviparous Onychophora. Most of the sites and individuals had previously been analysed using allozyme electrophoresis. A total of 157 peripatus collected at 54 sites throughout New Zealand were screened yielding 62 different haplotypes. Comparison of 540-bp COI sequences from Peripatoides revealed mean among-clade genetic distances of up to 11. 4% using Kimura 2-parameter (K2P) analysis or 17.5% using general time-reversible (GTR + I + Gamma) analysis. Phylogenetic analysis revealed eight well-supported clades that were consistent with the allozyme analysis. Five of the six cryptic peripatus species distinguished by allozymes were confirmed by mtDNA analysis. The sixth taxon appeared to be paraphyletic, but genetic and geographical evidence suggested recent speciation. Two additional taxa were evident from the mtDNA data but neither occurred within the areas surveyed using allozymes. Among the peripatus surveyed with both mtDNA and allozymes, only one clear instance of recent introgression was evident, even though several taxa occurred in sympatry. This suggests well-developed mate recognition despite minimal morphological variation and low overall genetic diversity.     

Phylogeography of the Qinghai–Tibet Plateau endemic alpine herb Pomatosace filicula (Primulaceae)

In order to trace the response of alpine plants on the Qinghai–Tibet Plateau (QTP) to the Quaternary climate oscillations, the phylogeographic history of Pomatosace filicula Maxim. was investigated in the present study. Based on sequence variations of two maternally inherited plastid markers, matK and trnH-psbA, and the biparentally inherited nuclear ribosomal internal transcribed spacer (nrITS), we estimated the population genetic structure, lineage divergence timescale, and population dynamics of P. filicula. Seven plastid haplotypes and two nrITS genotypes were identified across the range-wide sampling of 200 individuals from 24 populations. Although AMOVA revealed a high level of differentiation among populations (F_ST = 0.560), no significant phylogeographic structure was detected (N_ST = 0.503, G_ST = 0.518, P > 0.05). Molecular dating suggested that the divergences between major plastid lineages and nrITS genotypes occurred during the early and middle Pleistocene, and the middle Pleistocene, respectively. This species most likely survived at multiple unglaciated sites on the QTP during the Last Glacial Maximum, with most of these sites located above 4000 m a.s.l. The species probably experienced range expansion at its distribution fringe, but demographic tests did not suggest significant population size changes. We proposed that pronounced effective gene flow (N_em = 0.393) and short generation time may have obscured the phylogeographic and demographic patterns of this species. Our findings will shed new light on the Quaternary evolutionary history of the alpine flora of the QTP.     

Evolution and radiation in the scorpion Buthus elmoutaouakili Lourenco and Qi 2006 (Scorpiones: Buthidae) at the foothills of the Atlas Mountains (North Africa)

When low dispersal ability of an organism meets geographical barriers, the evolution of inter- and intraspecific differentiation is often facilitated. In the Atlas massif of North Africa, the genus Buthus splits into several species and diverges into numerous genetic lineages, often following the orographic structures of mountain systems. Such high mountain ranges often act as barriers for species with reduced mobility even on small spatial scales. To study the effect of orographic structures on organisms with low dispersal ability, we collected 61 individuals of the scorpion species Buthus elmoutaouakili at 18 locations around the southwestern foothills of the High Atlas and Antiatlas and in the Sousse valley (western Morocco). We analyzed intraspecific differentiation patterns within this geographically restricted area of about 100 × 50 km using 452 bp of the cytochrome oxidase I mitochondrial gene. We detected 5 distinct genetic lineages. In a second analysis, we added 61 previously published sequences from Buthus species from Europe and North Africa. Using a molecular clock approach, we detected old splits (4-5 Ma) separating the samples from 1) the western High Atlas and north of these mountains, 2) the Sousse valley and adjoining mountain areas, and 3) the southwestern Antiatlas. Further differentiation happened in the first 2 geographical groups about 3 Ma. Thus, the divergence time estimates based on a Bayesian approach support the onset of differentiation into these main clades along the Pliocene (5-2.3 Ma) when climatic oscillations started and a constant global cooling preceded the glacial-interglacial cycles of the Pleistocene. Further genetic splits into parapatric groups are detectable for the Sousse valley main group in the early Pleistocene. The climatic oscillations of the Pliocene and early Pleistocene might have caused repeated range shifts, expansions, and retractions leading to repeated vicariance, hereby producing the hierarchical structure of genetic differentiation in B. elmoutaouakili. A taxonomic revision, including morphological and molecular data, is needed to assess the status of each of these Buthus scorpion lineages.     

养分添加对天山高寒草地植物多样性和地上生物量的影响

为揭示高寒草地物种多样性和地上生物量以及二者之间关系对养分添加的响应模式, 该研究以天山高寒草地为对象, 通过两年的多重养分添加实验, 研究氮(N)、磷(P)、钾(K) 3种养分单独和组合添加对天山高寒草地群落物种多样性和地上生物量的影响。结果表明: (1)养分添加使当地植物物种多样性不同程度地减少, 其中以N + P、N + K、N + P + K添加的效应最为显著, 多重养分添加导致的土壤生态位维度降低是当地物种丧失的重要原因。(2)养分添加能显著提高群落地上生物量, 其中N为第一限制养分, 解除N限制后P和K成为限制养分, N + P + K复合添加对地上生物量的提高最为显著。(3)养分添加两年后, 地上生物量与物种丰富度之间无显著回归关系且地上生物量增加主要是由于禾草类生物量增加导致, 说明地上生物量主要由少数优势种决定而非群落物种数。     

Isolation and introgression in the Intermountain West: contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps)

Aim We studied the history of colonization, diversification and introgression among major phylogroups in the American pika, Ochotona princeps (Lagomorpha), using comparative and statistical phylogeographic methods. Our goal was to understand how Pleistocene climatic fluctuations have shaped the distribution of diversity at mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) loci in this alpine specialist. Location North America’s Intermountain West. Methods We accumulated mtDNA sequence data (c. 560–1700 bp) from 232 pikas representing 64 localities, and sequenced two nuclear introns (mast cell growth factor, c. 550 bp, n = 148; protein kinase C iota, c. 660 bp, n = 139) from a subset of individuals. To determine the distribution of major mtDNA lineages, we conducted a phylogenetic analysis on the mtDNA sequence data, and we calculated divergence times among the lineages using a Bayesian Markov chain Monte Carlo approach. Relationships among nuclear alleles were explored with minimum spanning networks. Finally, we conducted coalescent simulations of alternative models of population history to test for congruence between nDNA and mtDNA responses to Pleistocene glacial cycles. Results We found that: (1) all individuals could be assigned to one of five allopatric mtDNA lineages; (2) lineages are associated with separate mountain provinces; (3) lineages originated from at least two rounds of differentiation; (4) nDNA and mtDNA markers exhibited overall phylogeographic congruence; and (5) introgression among phylogroups has occurred at nuclear loci since their initial isolation. Main conclusions Pika populations associated with different mountain systems have followed separate but not completely independent evolutionary trajectories through multiple glacial cycles. Range expansion associated with climate cooling (i.e. glaciations) promoted genetic admixture among populations within mountain ranges. It also permitted periodic contact and introgression between phylogroups associated with different mountain systems, the record of which is retained at nDNA but not mtDNA loci. Evidence for different histories at nuclear and mtDNA loci (i.e. periodic introgression versus deep isolation, respectively) emphasizes the importance of multilocus perspectives for reconstructing complete population histories.     

Molecular Phylogeography and Population Genetic Structure of an Endangered Species Pachyhynobius shangchengensis (hynobiid Salamander) in a Fragmented Habitat of Southeastern China

The salamander Pachyhynobius shangchengensis (Hynobiidae) is a vulnerable species restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes in the Mount Dabieshan region in southeastern China. However, molecular phylogeography and population genetic structure of P. shangchengensis remain poorly investigated. In this study, we explored the genetic structure and phylogeography of P. shangchengensis based on partial sequences of the mitochondrial DNA (mtDNA) cytochrome b and cytochrome c oxidase subunit I genes. Fifty-one haplotypes and four clades were found among 93 samples. Phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographic regions separated by complicated topography and long distances. The distinct geographic distributions of all lineages and the estimated divergence time suggest spatial and temporal separation coinciding with climatic changes during the Pleistocene. Analysis of molecular variance indicated that most of the observed genetic variation occurred among the four groups, implying long-term interruption of gene flow, and the possible separation of P. shangchengensis into four management units for conservation.     

Molecular evidence for Pleistocene refugia at the eastern edge of the Tibetan Plateau

The role of the Quaternary ice ages in forming the contemporary genetic structure of populations has been well studied in a number of global regions. However, due to the different nature of glaciations and complex topography, their role in shaping eastern Eurasian genetic diversity, particular in areas surrounding the Tibetan Plateau have remained largely unstudied. We aimed to address this question by examining the genetic structure of an alpine forest-associated taxon, the blood pheasant (Ithaginis cruentus) to infer its phylogeographic history. We detected three phylogenetic lineages and four current population groups. By comparing molecular and palaeovegetation data, we found that major glaciations during the Pleistocene have had a major impact upon the current genetic diversity of this species. Coalescent simulations indicate that the populations retreated to different refugia during some glacial periods in the Pleistocene, but persisted through the last glacial maximum (LGM). The most significant recent population expansion was found to have occurred before the LGM, during which palaeoclimatic data indicate that the climate was both warmer and wetter than today. In contrast, during the LGM populations may have adopted an altitudinal shift strategy in order to track changes in alpine glaciers, exemplifying a general response for montane species in the region where alpine glaciations were not large enough to cause qualitative changes in vegetation. Although analysis based on a plumage related gene showed that divergent selection may have contributed to current patterns of intra-specific diversity, demographic isolation is inferred to have played a more dominant role.     

Molecular data and ecological niche modelling reveal the Pleistocene history of a semi‐aquatic bug (Microvelia douglasi douglasi) in East Asia

This study investigated the Pleistocene history of a semi‐aquatic bug, Microvelia douglasi douglasi Scott, 1874 (Hemiptera: Veliidae) in East Asia. We used M. douglasi douglasi as a model species to explore the effects of historical climatic fluctuations on montane semi‐aquatic invertebrate species. Two hypotheses were developed using ecological niche models (ENMs). First, we hypothesized that M. douglasi douglasi persisted in suitable habitats in southern Guizhou, southern Yunnan, Hainan, Taiwan and southeast China during the LIG. After that, the populations expanded (Hypothesis 1). As the spatial prediction in the LGM was significantly larger than in the LIG, we then hypothesized that the population expanded during the LIG to LGM transition (Hypothesis 2). We tested these hypotheses using mitochondrial data (COI+COII) and nuclear data (ITS1 + 5.8S+ITS2). Young lineages, relatively deep splits, lineage differentiation among mountain ranges in central, south and southwest China and high genetic diversities were observed in these suitable habitats. Evidence of mismatch distributions and neutrality tests indicate that a population expansion occurred in the late Pleistocene. The Bayesian skyline plot (BSP) revealed an unusual population expansion that likely happened during the cooling transition between LIG and LGM. The results of genetic data were mostly consistent with the spatial predictions from ENM, a finding that can profoundly improve phylogeographic research. The ecological requirements of M. douglasi douglasi, together with the geographical heterogeneity and climatic fluctuations of Pleistocene in East Asia, could have shaped this unusual demographic history. Our study contributes to our knowledge of semi‐aquatic bug/invertebrate responses to Pleistocene climatic fluctuations in East Asia.     

A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanic Daphnia populations in the Alps

Zooplanktonic microcrustaceans of the Daphnia pulex group appear highly differentiated at high altitudes as a result of alternative colonizations and quick local adaptation to harsh environments. In particular, the occurrence of deeply differentiated mountain lineages of European Daphnia pulicaria (EuPC) is highly related to glacial advances and retreats during the Pleistocene. Nowadays, one single ancient EuPC lineage survives in the Pyrenees, with another inhabiting the High Tatra Mountains. Much less is known about populations inhabiting the Alps, where EuPC populations are extremely rare. Recently, four new melanic populations have been discovered in lakes in the Western Italian Alps, offering the opportunity to study their origin and adaptations. We inferred phylogenetic relationships of melanic high‐mountain populations in order to disentangle their history and clarify the colonization patterns of alpine populations. Molecular data suggest that dark populations originated from at least two ancestors, one genetically close to boreal haplotypes, the other apparently related to refugial populations that survived in southern Europe. Therefore, dark pigmentation and obligate parthenogenesis evolved independently within both lineages inhabiting the studied lakes as extreme local adaptations to the alpine environment. Finally, since impacts of human‐related activities and climate changes on mountain species are known to be dramatic, we pose strong issues for the conservation of these extremely localized endemisms. © 2014 The Linnean Society of London     

Phylogeographic patterns and high levels of chloroplast DNA diversity in four Packera (asteraceae) species in southwestern Alberta

Chloroplast DNA (cpDNA) haplotype variation is compared among alpine and prairie/montane species of Packera from a region in southwestern Alberta that straddles the boundary of Pleistocene glaciation. The phylogeny of the 15 haplotypes identified reveals the presence of two groups: one generally found in coastal and northern species and the other from species in drier habitats. The presence of both groups in all four species and most populations from southwestern Alberta is evidence of past hybridization involving species or lineages that may no longer be present in the region. With the exception of the alpine P. subnuda (phiST = 1.0), interpopulational subdivision of haplotype variation is low (phiST < 0.350), suggesting that interpopulational gene flow is high. However, based on haplotype distribution patterns, we propose that Pleistocene hybridization and incomplete lineage sorting have resulted in reduced subdivision of interpopulational variation so that gene flow may not be as high as indicated. Drift has been more important in the alpine species populations, especially P. subnuda.     

Cladogenesis and phylogeography of the lizard Phrynocephalus vlangalii (Agamidae) on the Tibetan plateau

Phrynocephalus vlangalii is restricted to dry sand or Gobi desert highlands between major mountain ranges in the Qinghai (Tibetan) Plateau. Mitochondrial DNA (mtDNA) sequence (partial ND2, tRNA(Trp) and partial tRNA(Ala)) was obtained from 293 Phrynocephalus sampled from 34 sites across the plateau. Partitioned Bayesian and maximum parsimony phylogenetic analyses revealed that P. vlangalii and two other proposed species (P. erythrus and P. putjatia) together form a monophyletic mtDNA clade which, in contrast with previous studies, does not include P. theobaldi and P. zetangensis. The main P. vlangalli clade comprises seven well-supported lineages that correspond to distinct geographical areas with little or no overlap, and share a most recent common ancestor at 5.06 +/- 0.68 million years ago (mya). This is much older than intraspecific lineages in other Tibetan animal groups. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruption of maternal gene flow. A combined approach based on tests of population expansion, estimation of node dates, and significance tests on clade areas indicated that phylogeographical structuring has been primarily shaped by three main periods of plateau uplift during the Pliocene and Pleistocene, specifically 3.4 mya, 2.5 mya and 1.7 mya. These periods corresponded to the appearance of several mountain ranges that formed physical barriers between lineages. Populations from the Qaidam Basin are shown to have undergone major demographic and range expansions in the early Pleistocene, consistent with colonization of areas previously covered by the huge Qaidam palaeolake, which desiccated at this time. The study represents one of the most detailed phylogeographical analyses of the Qinghai Plateau to date and shows how geological events have shaped current patterns of diversity.     

Complex biogeographic patterns in Androsace (Primulaceae) and related genera: evidence from phylogenetic analyses of nuclear internal transcribed spacer and plastid trnL-F sequences

We conducted phylogenetic analyses of Androsace and the closely related genera Douglasia, Pomatosace, and Vitaliana using DNA sequences of the nuclear internal transcribed spacer (ITS) and the plastid trnL-F region. Analyses using maximum parsimony and Bayesian inference yield congruent relationships among several major lineages found. These lineages largely disagree with previously recognized taxonomic groups. Most notably, (1) Androsace sect. Andraspis, comprising the short-lived taxa, is highly polyphyletic; (2) Pomatosace constitutes a separate phylogenetic lineage within Androsace; and (3) Douglasia and Vitaliana nest within Androsace sect. Aretia. Our results suggest multiple origins of the short-lived lifeform and a possible reversal from annual or biennial to perennial habit at the base of a group that now contains mostly perennial high mountain or arctic taxa. The group containing Androsace sect. Aretia, Douglasia, and Vitaliana includes predominantly high alpine and arctic taxa with an arctic-alpine distribution, but is not found in the European and northeastern American Arctic or in Central and East Asia. This group probably originated in Europe in the Pliocene, from where it reached the amphi-Beringian region in the Pleistocene or late Pliocene.     

Biogeography,timing, and life-history traits in the PPAM clade: Coleanthinae (syn. Puccinelliinae), Poinae,Alopecurinae superclade,Miliinae, and Avenulinae and Phleinae (Poaceae,Pooideae, Poeae)

We conducted a biogeographic analysis of the PPAM clade of Poeae Plastid DNA Group 2, which includes 12 subtribes of C₃ grasses. One hundred and eighty-four species sampled represent 42 of 43 accepted genera and taxonomic diversity in large genera. We analyzed plastid sequences of matK, trnC-rpoB, and trnT-trnL-trnF using BEAST to produce a dated tree and MrBayes to produce a Bayesian tree, on which we ran Bayesian-Binary-Markov-Chain analyses on a worldwide biogeographic data set of 12 areas. PPAM split in southwestern Asia into subtribe Coleanthinae and PAM clades in the Early Miocene. PAM diversified rapidly in the Middle Miocene in southwestern Asia into four monogeneric lineages, Avenulinae, Phleinae, Miliinae, Poinae, and the Alopecurinae superclade (seven subtribes with 27 genera). In the Late Miocene, Pliocene, and mostly Pleistocene, the latter four lineages diversified and dispersed across Eurasia and established in North America. Dispersals to the southern hemisphere occurred in the Pliocene and Pleistocene. Annuals occur in 15 Mediterranean and southwestern Asia genera, but in few genera in other regions. Beyond phylogenetically isolated annual species dating to the Miocene, all other annuals evolved in the Pliocene and Pleistocene. Cold tolerance is high among perennial species, many occurring in the alpine, nine genera ranging into the Arctic. We suggest that alpine and subalpine habitats were ancestral. High tolerance of saline and alkaline conditions arose between the Pliocene and Pleistocene in Coleanthinae, Alopecurinae, Poinae, Hookerochloinae, Beckmanniinae, and Arctopoa. Combinations are proposed for Cornucopiae alopecuroides in Alopecurus and for Paracolpodium colchicum in Hyalopodium. A nothogenus × Catanellia is proposed for Catabrosa × Puccinellia.     

Niche shifts and range expansions along cordilleras drove diversification in a high‐elevation endemic plant genus in the tropical Andes

The tropical Andes represent one of the world's biodiversity hot spots, but the evolutionary drivers generating their striking species diversity still remain poorly understood. In the treeless high‐elevation Andean environments, Pleistocene glacial oscillations and niche differentiation are frequently hypothesized diversification mechanisms; however, sufficiently densely sampled population genetic data supporting this are still lacking. Here, we reconstruct the evolutionary history of Loricaria (Asteraceae), a plant genus endemic to the Andean treeless alpine zone, based on comprehensive population‐level sampling of 289 individuals from 67 populations across the entire distribution ranges of its northern Andean species. Partly incongruent AFLP and plastid DNA markers reveal that the distinct genetic structure was shaped by a complex interplay of biogeography (spread along and across the cordilleras), history (Pleistocene glacial oscillations) and local ecological conditions. While plastid variation documents an early split or colonization of the northern Andes by at least two lineages, one of which further diversified, a major split in the AFLP data correlate with altitudinal ecological differentiation. This suggests that niche shifts may be important drivers of Andean diversification not only in forest–alpine transitions, but also within the treeless alpine zone itself. The patterns of genetic differentiation at the intraspecific level reject the hypothesized separation in spatially isolated cordilleras and instead suggest extensive gene flow among populations from distinct mountain chains. Our study highlights that leveraging highly variable markers against extensive population‐level sampling is a promising approach to address mechanisms of rapid species diversifications.     

Local-scale environmental variation generates highly divergent lineages associated with stream drainages in a terrestrial salamander, Plethodon caddoensis

Spatial and temporal heterogeneity in environmental factors can have profound effects on diversification in species that are tightly linked to their environments. The Caddo Mountain Salamander (Plethodon caddoensis) inhabits a unique physiographic section of the Ouachita Mountains in central North America, a region in which Pleistocene climatic fluctuations have been implicated in driving lineage diversification in two other closely related salamanders. We examined P. caddoensis to determine whether it was similarly impacted by historic climatic changes and test whether physiographic features unique to the area also contributed to its diversification. We found that P. caddoensis is composed of four highly divergent, geographically distinct lineages that abut one another along an east-west axis. Phylogeographic structure was significantly related to both geographic distance and stream drainages, indicating that connectivity of streams and stream-associated habitats (e.g., talus) influence patterns of interpopulation gene flow. Lineages originated during the Middle Miocene and population size decreased in all lineages during the Pleistocene. Surface Geology and precipitation were the most important variables predicting the species distribution. Our results show that the unique physiographic features of the area coupled with species response to climatic factors have driven lineage diversification and phylogeographic structure in P. caddoensis. Variation in responses to historic climatic fluctuations among salamander species in this region underscore the importance of integrating species ecology with other factors such as geology and hydrology in order to better understand the effects of climate change on species with close associations to their environments.