Survival in northern microrefugia in an endemic Carpathian gammarid (Crustacea: Amphipoda)

Gammarus leopoliensis (Crustacea: Amphipoda) is considered a north‐eastern Carpathian endemic species and therefore can be regarded as an appropriate model for testing the hypothesis of Quaternary glacial survival in northern microrefugia. However, 250 km south, the south‐western Carpathians harbour populations that resemble phenotypically both G. leopoliensis and Gammarus kischineffensis, a similar species distributed east of the Carpathians. We used maximum‐likelihood and Bayesian methods to evaluate the phylogenetic relationships of these three taxa based on mitochondrial and nuclear markers, and quantitatively compared diversity patterns, phylogeography and divergence times among north‐eastern and south‐western Carpathian taxa. Results indicate that G. leopoliensis and the south‐western populations form together a strongly supported group (G. leopoliensis s.l.) which, along with G. kischineffensis, belongs to the Gammarus balcanicus clade. This group contains 12 lineages mainly of Pliocene age. G. leopoliensis consists of two widely distributed and recently expanded allopatric sister lineages that diverged from the southern ones ca. 4 Ma, indicating long‐term survival in northern microrefugia. The southern lineages are micro‐endemic and display a scattered distribution, suggesting a more ancient, relict pattern. We conclude that the contrasting diversity patterns between the disjunct distributional areas of G. leopoliensis s.l. reflect differential survival of lineages across the latitudinal gradient, offering a promising system for comparing the evolutionary ecology of lineages persisting in latitudinally disconnected microrefugia. These results fill an important gap in the knowledge of European gammarid biogeography and reveal that all Carpathian Gammarus taxa are ancient and diverse species complexes.     

A biogeographical profile of the sand cockroach Arenivaga floridensis and its bearing on origin hypotheses for Florida scrub biota

Florida scrub is a xeric ecosystem associated with the peninsula's sand ridges, whose intermittent Pliocene–Pleistocene isolation is considered key to scrub endemism. One scrub origin hypothesis posits endemics were sourced by the Pliocene dispersal of arid‐adapted taxa from southwestern North America; a second invokes Pleistocene migration within eastern North America. Only one study to date has explicitly tested these competing hypotheses, supporting an eastern origin for certain scrub angiosperms. For further perspective, we conducted a genetic analysis of an endemic arthropod, the Florida sand cockroach (Arenivaga floridensis), with two aims: (1) to reconstruct the peninsular colonization and residence history of A. floridensis and (2) determine whether its biogeographic profile favors either origin hypothesis. We sequenced the cox2 mitochondrial gene for 237 specimens (65 populations) as well as additional loci (cox1, nuclear H3) for a subset of Florida roaches and congeners. Using Network and Bayesian inference methods, we identified three major lineages whose genetic differentiation and phylogeographical structure correspond with late Pliocene peninsula insularization, indicating Arenivaga was present and broadly distributed in Florida at that time. Stem and crown divergence estimates (6.36 Ma; 2.78 Ma) between A. floridensis and western sister taxa span a period of extensive dispersal by western biota along an arid Gulf Coast corridor. These phylogeographical and phylogenetic results yield a biogeographic profile consistent with the western origin hypothesis. Moreover, age estimates for the roach's peninsular residence complement those of several other endemics, favoring a Pliocene (or earlier) inception of the scrub ecosystem. We argue that eastern versus western hypotheses are not mutually exclusive; rather, a composite history of colonization involving disparate biotas better explains the diverse endemism of Florida scrub.     

Wider sampling reveals a non‐sister relationship for geographically contiguous lineages of a marine mussel

The accuracy of phylogenetic inference can be significantly improved by the addition of more taxa and by increasing the spatial coverage of sampling. In previous studies, the brown mussel Perna perna showed a sister–lineage relationship between eastern and western individuals contiguously distributed along the South African coastline. We used mitochondrial (COI) and nuclear (ITS) sequence data to further analyze phylogeographic patterns within P. perna. Significant expansion of the geographical coverage revealed an unexpected pattern. The western South African lineage shared the most recent common ancestor (MRCA) with specimens from Angola, Venezuela, and Namibia, whereas eastern South African specimens and Mozambique grouped together, indicating a non‐sister relationship for the two South African lineages. Two plausible biogeographic scenarios to explain their origin were both supported by the hypotheses‐testing analysis. One includes an Indo‐Pacific origin for P. perna, dispersal into the Mediterranean and Atlantic through the Tethys seaway, followed by recent secondary contact after southward expansion of the western and eastern South African lineages. The other scenario (Out of South Africa) suggests an ancient vicariant divergence of the two lineages followed by their northward expansion. Nevertheless, the “Out of South Africa” hypothesis would require a more ancient divergence between the two lineages. Instead, our estimates indicated that they diverged very recently (310 kyr), providing a better support for an Indo‐Pacific origin of the two South African lineages. The arrival of the MRCA of P. perna in Brazil was estimated at 10 [0–40] kyr. Thus, the hypothesis of a recent introduction in Brazil through hull fouling in wooden vessels involved in the transatlantic itineraries of the slave trade did not receive strong support, but given the range for this estimate, it could not be discarded. Wider geographic sampling of marine organisms shows that lineages with contiguous distributions need not share a common ancestry.     

Evolutionary insights into the North American Necturus beyeri complex (Amphibia: Caudata) based on molecular genetic and morphological analyses

Necturus beyeri (Caudata: Proteidae), as conceived by some, contains paedomorphic salamanders distributed from the Ochlockonee drainage of Florida to the Angelina drainage of Texas. Because these salamanders differ in color pattern and karyotype across their geographic range, we performed a phylogeographic analysis that included representatives from all major drainages as well as of all congeners. The mitochondrially encoded ND2 gene was used to infer phylogenetic relationships using Bayesian inference. Morphometrics of head shape were analyzed and included as an independent data set. Our work suggests that Necturus comprises 11 lineages. A basal split within the genus separates an ancestor of two Atlantic Coastal Plain species (Necturus lewisi and Necturus punctatus) from the ancestor of nine distinct Gulf Coastal Plain lineages. One lineage is consistent with Necturus alabamensis, a species currently recognized in the Black Warrior drainage of Alabama. Two lineages comprise Necturus maculosus, as historically recognized, and six lineages comprise N. beyeri, as recognized by some, each of which occupies a unique drainage. Both of these species are demonstrated to be paraphyletic. Head morphometrics show the same patterns as the mtDNA. Overall, lineages within Necturus exhibit an east‐to‐west progression of appearance on the phylogenetic trees. This pattern corroborates biogeographic hypotheses based on previous karyological work. Within N. beyeri, this progression separates a pattern class of two eastern lineages lacking bold spotting and possessing relatively small mean body lengths from a pattern class of four western lineages possessing bold spotting and larger mean body sizes. Thus, the two eastern lineages of N. beyeri are similar in color pattern and body size to N. punctatus either through retention of the ancestral color pattern and size for the genus or through convergent selection in eastern streams of the Gulf Coastal Plain.     

Phylogeography of the pallid kangaroo mouse,Microdipodops pallidus: a sand‐obligate endemic of the Great Basin,western North America

Aim Kangaroo mice, genus Microdipodops Merriam, are endemic to the Great Basin and include two species: M. pallidus Merriam and M. megacephalus Merriam. The pallid kangaroo mouse, M. pallidus, is a sand‐obligate desert rodent. Our principal intent is to identify its current geographical distribution and to formulate a phylogeographical hypothesis for this taxon. In addition, we test for orientation patterns in haplotype sharing for evidence of past episodes of movement and gene flow. Location The Great Basin Desert region of western North America, especially the sandy habitats of the Lahontan Trough and those in south‐central Nevada. Methods Mitochondrial DNA sequence data from portions of three genes (16S ribosomal RNA, cytochrome b, and transfer RNA for glutamic acid) were obtained from 98 individuals of M. pallidus representing 27 general localities sampled throughout its geographical range. Molecular sequence data were analysed using neighbour‐joining, maximum‐parsimony, maximum‐likelihood and Bayesian methods of phylogenetic inference. Directional analysis of phylogeographical patterns, a novel method, was used to examine angular measurements of haplotype sharing between pairs of localities to detect and quantify historical events pertaining to movement patterns and gene flow. Results Collecting activities showed that M. pallidus is a rather rare rodent (mean trapping success was 2.88%), and its distribution has changed little from that determined three‐quarters of a century ago. Two principal phylogroups, distributed as eastern and western moieties, are evident from the phylogenetic analyses (mean sequence divergence for cytochrome b is c. 8%). The western clade shows little phylogenetic structure and seems to represent a large polytomy. In the eastern clade, however, three subgroups are recognized. Nine of the 42 unique composite haplotypes are present at two or more localities and are used for the orientation analyses. Axial data from haplotype sharing between pairwise localities show significant, non‐random angular patterns: a north‐west to south‐east orientation in the western clade, and a north‐east to south‐west directional pattern in the eastern clade. Main conclusions The geographical range of M. pallidus seems to be remarkably stable in historical times and does not show a northward (or elevationally upward) movement trend, as has been reported for some other kinds of organism in response to global climate change. The eastern and western clades are likely to represent morphologically cryptic species. Estimated times of divergence of the principal clades of M. pallidus (4.38 Ma) and between M. pallidus and M. megacephalus (8.1 Ma; data from a related study) indicate that kangaroo mice diverged much earlier than thought previously. The phylogeographical patterns described here may serve as a model for other sand‐obligate members of the Great Basin Desert biota.     

Phylogeography of Sophora davidii (Leguminosae) across the ‘Tanaka‐Kaiyong Line’, an important phytogeographic boundary in Southwest China

The ‘Tanaka‐Kaiyong Line’ (TKL) is a major phytogeographic boundary in Southwest China, separating East Asia's Sino‐Himalayan and Sino‐Japanese Floras. However, little is known about the importance of this boundary in promoting intraspecific phylogeographic subdivision and divergence. Using chloroplast (cpDNA) and nuclear‐intron (nDNA) sequence data, we reconstructed the population history of Sophora davidii, a drought‐tolerant riparian shrub widely distributed on either side of the TKL. Specifically, we aimed at testing two long‐standing explanations for possible vicariant events across the TKL: (i) Late Pliocene (c. 3 Ma) geological uplift of the eastern Qinghai‐Tibetan Plateau (QTP) or (ii) a sharp environmental gradient associated with the establishment of different monsoon regimes on either side of the TKL during the (Late) Pleistocene. Our genealogical analyses detected a major west–east split in cpDNA, geographically largely consistent with the TKL, and dated to c. 1.28 Ma (95% HPD: 0.21–2.96 Ma), hence postdating the latest phase of eastern QTP uplift. Furthermore, integrating cpDNA phylogeographic patterns with mismatch analyses, we found multiple refugial isolation and long‐term demographic stability of populations in the west (Hengduan Mountain Range) compared with extensive range expansions in the east, possibly during the last glacial period(s) and followed by differentiation into regional sublineages (southeast: Yunnan‐Guizhou Plateau vs. northeast: Qinling Mts./Loess Plateau). Although nuclear differentiation was less marked, the geographical pattern of nDNA haplotypes provided some further indication of the species' eastward expansion, possibly from source populations located just east of the TKL (lower Jinshajiang region). Overall, the present data reject the geological (tectonic) explanation for the TKL and, instead, provide supportive evidence for its role as a climatically driven barrier to present‐day plant dispersal. In addition, our study highlights changing temperatures and vegetation types during the last glacial period(s), along with aspects of regional topography, to be important determinants of the glacial eastward expansion of S. davidii. In consequence, our study lends support to a ‘glacial out‐of‐Hengduan Mts’. hypothesis for the xerophytic‐riparian flora of Southwest China, which in turn is inconsistent with the traditional view of the TKL as a ‘classical’ vicariant‐biogeographic boundary.     

Climatic drivers of leaf traits and genetic divergence in the tree Annona crassiflora: a broad spatial survey in the Brazilian savannas

The Cerrado is the largest South American savanna and encompasses substantial species diversity and environmental variation. Nevertheless, little is known regarding the influence of the environment on population divergence of Cerrado species. Here, we searched for climatic drivers of genetic (nuclear microsatellites) and leaf trait divergence in Annona crassiflora, a widespread tree in the Cerrado. The sampling encompassed all phytogeographic provinces of the continuous area of the Cerrado and included 397 individuals belonging to 21 populations. Populations showed substantial genetic and leaf trait divergence across the species' range. Our data revealed three spatially defined genetic groups (eastern, western and southern) and two morphologically distinct groups (eastern and western only). The east‐west split in both the morphological and genetic data closely mirrors previously described phylogeographic patterns of Cerrado species. Generalized linear mixed effects models and multiple regression analyses revealed several climatic factors associated with both genetic and leaf trait divergence among populations of A. crassiflora. Isolation by environment (IBE) was mainly due to temperature seasonality and precipitation of the warmest quarter. Populations that experienced lower precipitation summers and hotter winters had heavier leaves and lower specific leaf area. The southwestern area of the Cerrado had the highest genetic diversity of A. crassiflora, suggesting that this region may have been climatically stable. Overall, we demonstrate that a combination of current climate and past climatic changes have shaped the population divergence and spatial structure of A. crassiflora. However, the genetic structure of A. crassiflora reflects the biogeographic history of the species more strongly than leaf traits, which are more related to current climate.     

Population structure and phylogeography reveal pathways of colonization by a migratory marine reptile (Chelonia mydas) in the central and eastern Pacific

Climate, behavior, ecology, and oceanography shape patterns of biodiversity in marine faunas in the absence of obvious geographic barriers. Marine turtles are an example of highly migratory creatures with deep evolutionary lineages and complex life histories that span both terrestrial and marine environments. Previous studies have focused on the deep isolation of evolutionary lineages (>3 mya) through vicariance; however, little attention has been given to the pathways of colonization of the eastern Pacific and the processes that have shaped diversity within the most recent evolutionary time. We sequenced 770 bp of the mtDNA control region to examine the stock structure and phylogeography of 545 green turtles from eight different rookeries in the central and eastern Pacific. We found significant differentiation between the geographically separated nesting populations and identified five distinct stocks (F_ST = 0.08–0.44, P < 0.005). Central and eastern Pacific Chelonia mydas form a monophyletic group containing 3 subclades, with Hawaii more closely related to the eastern Pacific than western Pacific populations. The split between sampled central/eastern and western Pacific haplotypes was estimated at around 0.34 mya, suggesting that the Pacific region west of Hawaii has been a more formidable barrier to gene flow in C. mydas than the East Pacific Barrier. Our results suggest that the eastern Pacific was colonized from the western Pacific via the Central North Pacific and that the Revillagigedos Islands provided a stepping‐stone for radiation of green turtles from the Hawaiian Archipelago to the eastern Pacific. Our results fit with a broader paradigm that has been described for marine biodiversity, where oceanic islands, such as Hawaii and Revillagigedo, rather than being peripheral evolutionary “graveyards”, serve as sources and recipients of diversity and provide a mechanism for further radiation.     

Variable phylogeographic histories of five forest birds with populations in Upper and Lower Guinea: implications for taxonomy and evolutionary conservation

This study evaluates phylogeographic structure in selected forest bird species distributed on either side of the Dahomey Gap in West Africa to extend analyses of avian diversification across the Guineo-Congolean forest. Mitochondrial DNA sequence data were collected for five species, including four with a break in distribution across the Dahomey Gap and one with a more continuous distribution. Data for the five focal species were included in a single analysis along with appropriate outgroup taxa, allowing estimates of divergence time on a common timescale. Both phylogeographic patterns and estimated divergence times were highly variable. In two cases (Green Hylia Hylia prasina and Yellow-whiskered Greenbul Eurillas latirostris), samples from east and west of the Dahomey Gap belong to divergent mitochondrial lineages, but with substantially older divergence in Eurillas (～4.1 MY). In Western Bluebill Spermophaga haematina, relatively divergent eastern and western lineages (～1.1 MY) were sampled in the same locality in eastern Ghana, suggesting east to west gene flow across the gap following earlier vicariance. In Forest Robin Stiphrornis erythrothorax, birds sampled within Ghana were from two highly divergent lineages (～1.9 MY), one of which is more closely related to birds from Cameroon and Equatorial Guinea, such that divergence across the Dahomey Gap was comparatively recent (～0.36 MY). For both Hylia and Stiphrornis, we corroborate recent studies documenting multiple divergent lineages within each genus, some of which may represent distinct species. Consistent with previous studies, our analysis shows that the Dahomey Gap can be a significant barrier to gene flow for species restricted to forest habitats. At the same time, individual species exhibit a broad range of divergence times and phylogeographic histories of variable complexity. We discuss the taxonomic implications of our results for each focal species.     

Deep divergence among mitochondrial lineages in African jackals

Recently, molecular analyses revealed that African and Eurasian golden jackals are distinct species. This finding suggests re‐investigation of the phylogenetic relationships and taxonomy of other African members of the Canidae. Here, we provide a study on the phylogenetic relationship between populations of African jackals Lupulella mesomelas and L. adusta inferred from 962 bp of the mitochondrial cytochrome b (cytb) gene. As expected from its disjunct distribution, with one population in eastern Africa and the other one in southern Africa, we found two mitochondrial lineages within L. mesomelas, which diverged about 2.5 million years ago (Ma). In contrast, in L. adusta with its more continuous distribution in sub‐Saharan Africa, we found only a shallower genetic diversification, with the exception of the West African population, which diverged around 1.4 Ma from the Central and East African populations. Both divergence ages are older than, for example the 1.1–0.9 million years between the grey wolf Canis lupus and the African golden wolf C. lupaster. One taxonomic implication of our findings might be that the two L. mesomelas populations warrant species status. However, genome‐wide data with adequate geographical sampling are needed to substantiate our results.     

Ecological divergence and speciation between lemur (Eulemur) sister species in Madagascar

Understanding ecological niche evolution over evolutionary timescales is crucial to elucidating the biogeographic history of organisms. Here, we used, for the first time, climate‐based ecological niche models (ENMs) to test hypotheses about ecological divergence and speciation processes between sister species pairs of lemurs (genus Eulemur) in Madagascar. We produced ENMs for eight species, all of which had significant validation support. Among the four sister species pairs, we found nonequivalent niches between sisters, varying degrees of niche overlap in ecological and geographic space, and support for multiple divergence processes. Specifically, three sister‐pair comparisons supported the null model that niches are no more divergent than the available background region. These findings are consistent with an allopatric speciation model, and for two sister pairs (E. collaris–E. cinereiceps and E. rufus–E. rufifrons), a riverine barrier has been previously proposed for driving allopatric speciation. However, for the fourth sister pair E. flavifrons–E. macaco, we found support for significant niche divergence, and consistent with their parapatric distribution on an ecotone and the lack of obvious geographic barriers, these findings most strongly support a parapatric model of speciation. These analyses thus suggest that various speciation processes have led to diversification among closely related Eulemur species.     

Evolutionary history of an alpine shrub Hippophae tibetana (Elaeagnaceae): allopatric divergence and regional expansion

Increasing evidence suggests that geological or climatic events in the past promoted allopatric speciation of alpine plants in the Qinghai‐Tibetan Plateau and adjacent region. However, few studies have been undertaken to examine whether such allopatric divergences also occurred within a morphologically uniform species. In the present study, we report the evolutionary history of an alpine shrub species, Hippophae tibetana, based on examining chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variations. We sequenced two cpDNA fragments (trnL‐F and trnS‐G) and the nuclear ITS region in 183 individuals collected from 21 natural populations. Ten chlorotypes and 17 ITS types were identified. Phylogenetic analyses of both chlorotypes and ITS sequence variations suggested two distinct lineages distributed in the eastern and western region, respectively. On the basis of the fast and low plant substitution rates, these two lineages were estimated to have diverged from each other between 1 and 4 million years ago, during the period of the major glaciations and orogenic processes. In addition, ITS has undergone the accelerated evolution in two populations in the southern Himalaya isolated by the high mountains with a surprising accumulation of the private variations. The east–west split was also supported by an analysis of molecular variance, which partitioned around 91% of the total cpDNA variance between these two groups of populations. A single chlorotype was found for most populations in eastern or western region, suggesting a recent postglacial expansion within each region. Star‐phylogeny and mismatch analyses of all chlorotypes within the eastern group of populations suggested an earlier regional expansion before the Last Glacial Maximum (LGM). The local fixture of the different chlorotypes in multiple populations suggested more than one refugia remained for eastern or western region. Coalescent tests rejected the hypothesis that all current populations originated from a single refugium during the LGM. Instead, they supported hypothesis that two lineages diverged before the late Pleistocene. These findings, when taken together, suggested that this species had experienced long allopatric divergence and recent regional range expansions in response to orogenic processes and the climate changes. The evolutionary history of this shrub species highlights importance of geographical isolations to the intraspecific divergence of alpine plants occurring in the world's ruff. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 37–50.     

Phylogeography of the Northern Alligator Lizard (Squamata,Anguidae): Hidden diversity in a western endemic

Western North America includes the California Floristic Province and the Pacific Northwest, biologically diverse regions highlighted by a complex topography, geology, climate and history. A number of animals span these regions and show distinctive patterns of dispersal, vicariance and lineage diversification. Examining phylogeographic patterns in the fauna of this area aids in our understanding of the forces that have contributed to the generation and maintenance of regional biodiversity. Here, we investigate the biogeography and population structure of the Northern Alligator Lizard (Elgaria coerulea), a wide‐ranging anguid endemic to western North America. We sequenced two mtDNA fragments (ND2 and ND4) for 181 individuals across the range of the species and analysed these data with phylogenetic approaches to infer population and biogeographic history, and date major divergences within the taxon. We further used Bayesian clustering methods to assess major patterns of population structure and performed ecological niche modelling (ENM) to aid in our interpretation of geographic structure and diversification of E. coerulea lineages. Our phylogeographic examination of E. coerulea uncovered surprising diversity and structure, recovering 10 major lineages, each with substantial geographic substructure. While some divergences within the species are relatively old (Pliocene, 5.3–2.6 mya), most intraspecific variation appears to be of more recent origin (Pleistocene, 2.6 mya‐11,700 ya). Current diversity appears to have arisen in the Sierra Nevada Mountains and spread west and north since the Pliocene. Finally, our ENMs suggest that much of the Coast Ranges in California provided ideal habitat during the Last Glacial Maxima (LGM) that has since contracted dramatically and shifted northwards, whereas significant portions of the Sierra Nevada were unsuitable during the LGM and have since become more suitable. Interestingly, E. coerulea shares a number of genetic boundaries with other sympatric taxa, suggesting common historical events and geomorphological features have shaped the biota of this region.     

The east‐west‐north colonization history of the Mediterranean and Europe by the coastal plant Carex extensa (Cyperaceae)

Coastal plants are ideal models for studying the colonization routes of species because of the simple linear distributions of these species. Carex extensa occurs mainly in salt marshes along the Mediterranean and European coasts. Variation in cpDNA sequences, amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs) of 24 populations were analysed to reconstruct its colonization history. Phylogenetic relationships indicate that C. extensa together with the South American Carex vixdentata and the southern African Carex ecklonii form a monophyletic group of halophilic species. Analyses of divergence times suggest that early lineage diversification may have occurred between the late Miocene and the late Pliocene (Messinian crisis). Phylogenetic and network analyses of cpDNA variation revealed the monophyly of the species and an ancestral haplotype contained in populations of the eastern Mediterranean. The AFLP and SSR analyses support a pattern of variation compatible with these two lineages. These analyses also show higher levels of genetic diversity and differentiation in the eastern population group, which underwent an east‐to‐west Mediterranean colonization. Quaternary climatic oscillations appear to have been responsible for the split between these two lineages. Secondary contacts may have taken place in areas near the Ligurian Sea in agreement with the gene flow detected in Corsican populations. The AFLP and SSR data accord with the ‘tabula rasa’ hypothesis in which a recent and rapid colonization of northern Europe took place from the western Mediterranean after the Last Glacial Maximum. The unbalanced west‐east vs. west‐north colonization may be as a result of ‘high density blocking’ effect.     

The combined use of raw and phylogenetically independent methods of outlier detection uncovers genome‐wide dynamics of local adaptation in a lizard

Local adaptation is a dynamic process by which different allele combinations are selected in different populations at different times, and whose genetic signature can be inferred by genome‐wide outlier analyses. We combined gene flow estimates with two methods of outlier detection, one of them independent of population coancestry (CIOA) and the other one not (ROA), to identify genetic variants favored when ecology promotes phenotypic convergence. We analyzed genotyping‐by‐sequencing data from five populations of a lizard distributed over an environmentally heterogeneous range that has been changing since the split of eastern and western lineages ca. 3 mya. Overall, western lizards inhabit forest habitat and are unstriped, whereas eastern ones inhabit shrublands and are striped. However, one population (Lerma) has unstriped phenotype despite its eastern ancestry. The analysis of 73,291 SNPs confirmed the east–west division and identified nonoverlapping sets of outliers (12 identified by ROA and 9 by CIOA). ROA revealed ancestral adaptive variation in the uncovered outliers that were subject to divergent selection and differently fixed for eastern and western populations at the extremes of the environmental gradient. Interestingly, such variation was maintained in Lerma, where we found high levels of heterozygosity for ROA outliers, whereas CIOA uncovered innovative variants that were selected only there. Overall, it seems that both the maintenance of ancestral variation and asymmetric migration have counterbalanced adaptive lineage splitting in our model species. This scenario, which is likely promoted by a changing and heterogeneous environment, could hamper ecological speciation of locally adapted populations despite strong genetic structure between lineages.     

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak,Quercus lobata Née

Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate‐based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present compared with large‐scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28–1622)] and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time. In accordance with neutral expectations for stable populations, nuclear microsatellite diversity positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses. Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (16% vs. 11–18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion–contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions.     

Origin and dispersal of Potamophylax cingulatus (Trichoptera: Limnephilidae) in Iceland

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A Plains‐wanderer (Pedionomidae) that did not wander plains: a new species from the Oligocene of South Australia

The remarkable fauna of Australia evolved in isolation from other landmasses for millions of years, yet understanding the evolutionary history of endemic avian lineages on the continent is confounded by the ability of birds to disperse over geographical barriers even after vicariance events. The Plains‐wanderer Pedionomus torquatus (Charadriiformes) is an enigmatic, predominantly sedentary, quail‐like bird that occurs exclusively in sparse native grasslands of southeastern Australia. It is the only known species of its family (Pedionomidae), and its closest relatives are the South American seedsnipes (Thinocoridae). Here we describe a further representative of this lineage, Oligonomus milleri gen. et sp. nov., from the Late Oligocene of South Australia (26–24 Ma), which pre‐dates the earliest record of P. torquatus by c. 22 Ma and attests to the presence of this lineage during Australia's period of isolation (50–15 Ma). Based on the morphology of the coracoid and the palynological record, we propose that O. milleri and P. torquatus were ecologically disparate taxa and that, similar to coeval marsupials, O. milleri inhabited well‐wooded habitats, suggesting that the preference for grassland in the extant P. torquatus and thinocorids is likely to be convergent and not ancestral. The speciation event leading to the evolution of the extant Plains‐wanderer was probably triggered by the spread of grasslands across Australia in the Late Miocene–Pliocene, which this record pre‐dates. The presence of a pedionomid in the Late Oligocene of Australia strengthens the hypothesis of a Gondwanan divergence of the lineages giving rise to Thinocoridae and Pedionomidae.     

Varying levels of clonality and ploidy create barriers to gene flow and challenges for conservation of an Australian arid‐zone ecosystem engineer,Acacia loderi

Acacia loderi, the ecosystem engineer of the endangered Acacia loderi Shrublands in arid eastern Australia, spans a persistent (> 15 000 year) but poorly studied landscape feature, the Darling River. We investigated the genetic structure of 19 stands of eight to > 1000 plants separated by < 300 km to test for variation in life histories between semi‐arid and arid stands to the east and west of the Darling River, respectively. Eight of nine stands east of the Darling were exclusively sexual, whereas most of those to the west were clonal. Three western stands were monoclonal, two were polyploid, and one was a diverse mix of diploid and triploid phenotypes. Bayesian analysis revealed a complex genetic structure within the western stands, whereas the eastern stands formed only two genetic clusters. Conservation of small stands may require augmentation of genotypic diversity. However, most genotypic diversity resides within the eastern stands. Although arid zone stands of A. loderi are not always clonal, clonality and polyploidy are more common in the arid west. Clear demarcation of life histories either side of the Darling River may reflect ancient or contemporary effects of physical disturbance associated with the river channel, or cryptic environmental differences, with sexual and asexual reproduction, respectively, at a selective premium in the semi‐arid east and arid west. The restricted distribution of clones and variation in clonality and polyploidy suggests that smaller stands may be vulnerable and warrant individual management.     

Combining ecological niche modelling and morphology to assess the range‐wide population genetic structure of bobcats (Lynx rufus)

Despite a broad distribution, general habitat requirements, and a large dispersal potential, bobcats (Lynx rufus) exhibit a genetic division that longitudinally transects central North America. We investigated (1) whether the climate of the Last Glacial Maximum (LGM; 21 kya) isolated bobcats into refugia and also whether the current climate influences gene flow between the segregate populations and (2) whether the geographical patterns in cranial morphology reflect population identity. We created ecological niche models (ENMs) to evaluate climatic suitability and to estimate distributions of the disparate populations under both historical (LGM) and contemporary conditions. We used two‐dimensional geometric morphometric methods to evaluate variations in the cranium and mandible. These variations were then regressed across geographical variables to assess morphological differences throughout the range of the bobcat. ENMs projected onto LGM climate provided evidence of refugia during the LGM via increased suitability in the north‐west and south‐east portions of this species' range. Contemporarily, our models suggest that the Great Plains may be restricting bobcat migration and gene flow, effectively maintaining disparate populations. Morphological analyses identified a significant linear trend in shape variation across latitudinal and longitudinal gradients rather than distinct morphological divergence between lineages. Similar shape variations, however, did converge in approximate locations of assumed refugia. The findings of the present study provide a robust assessment of the biogeographical considerations for the population genetic structure of bobcats.