Cirques of the Southeastern Tibetan Plateau and Their Links to Climatic and Non-Climatic Factors

Cirque morphology is used to reflect the patterns of paleoclimate, paleoglaciation, and landscape evolution. Cirque study has been conducted in the Gangdise Mountains of the southern Tibetan Plateau (TP) and the central TP (dominated by a weak Indian summer monsoon (ISM) or a continental climate). This study focused on the cirques in the southeastern TP, which is dominated by a strong ISM, to analyse the controlling factors on cirque morphology. A total of 361 cirques were mapped in the Taniantaweng Range of the southeastern TP, and their metrics were calculated. The results showed that the cirque sizes increased with temperature and decreased with precipitation, which may be due to the development of valley-type glaciers and the effect of non-climatic factors. The cirques tended to face NE, implying that they prefer leeward slopes, and they were under the 'morning-afternoon' effect. With altitude, the tendency of the cirque aspect shifted from N to SE, and the cirque size decreased. The former may indicate the ability of the high altitude to support cirque development on climatically unfavourable slopes; the latter may be due to the development of valley-type glaciers or insufficient space for cirque development. The cirque size and shape did not show statistical differences between aspects. The cirques on soft bedrocks had larger heights than those on hard bedrocks, indicating that soft bedrocks promote subglacial erosion. A comparison with the results of the western, central, and eastern sectors of the Gangdise Mountains and the central TP reveals that the strength of the ISM did not necessarily increase the cirque density but limited the cirque size on a regional scale. The CFA did not show a reverse relationship with precipitation, but it showed a positive correlation with the cirque Z_mean, which implies that the CFA was greatly affected by altitude, and its distribution does not always reflect paleoclimatic patterns.

Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains

The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGM_L , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 meters apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGM_L glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.

Strong and lasting impacts of past global warming on baleen whales and their prey

Global warming is affecting the population dynamics and trophic interactions across a wide range of ecosystems and habitats. Translating these real-time effects into their long-term consequences remains a challenge. The rapid and extreme warming period that occurred after the Last Glacial Maximum (LGM) during the Pleistocene-Holocene transition (7-12 thousand years ago) provides an opportunity to gain insights into the long-term responses of natural populations to periods with global warming. The effects of this post-LGM warming period have been assessed in many terrestrial taxa, whereas insights into the impacts of rapid global warming on marine taxa remain limited, especially for megafauna. In order to understand how large-scale climate fluctuations during the post-LGM affected baleen whales and their prey, we conducted an extensive, large-scale analysis of the long-term effects of the post-LGM warming on abundance and inter-ocean connectivity in eight baleen whale and seven prey (fish and invertebrates) species across the Southern and the North Atlantic Ocean; two ocean basins that differ in key oceanographic features. The analysis was based upon 7032 mitochondrial DNA sequences as well as genome-wide DNA sequence variation in 100 individuals. The estimated temporal changes in genetic diversity during the last 30,000 years indicated that most baleen whale populations underwent post-LGM expansions in both ocean basins. The increase in baleen whale abundance during the Holocene was associated with simultaneous changes in their prey and climate. Highly correlated, synchronized and exponential increases in abundance in both baleen whales and their prey in the Southern Ocean were indicative of a dramatic increase in ocean productivity. In contrast, the demographic fluctuations observed in baleen whales and their prey in the North Atlantic Ocean were subtle, varying across taxa and time. Perhaps most important was the observation that the ocean-wide expansions and decreases in abundance that were initiated by the post-LGM global warming, continued for millennia after global temperatures stabilized, reflecting persistent, long-lasting impacts of global warming on marine fauna.

Genetic variation of the relict maple Acer miyabei: uncovering its history of disjunct occurrence and the role of mountain refugia in shaping genetic diversity

PREMISE

Relict species provide valuable insights into the origin and formation of extant vegetation. Here, we aimed to elucidate the genetic structure and diversity of a riparian relic, Acer miyabei, in Japan. Once widely distributed, it now occurs in three isolated regions. The most northern regional group is located at low elevation on Hokkaido Island, whereas the southernmost group in central Honshu Island is at high elevation in a mountainous landscape. This contrastive distribution enables us to examine the effects of climate oscillations on genetic diversity in relation to topographic variation.

METHODS

We collected 604 individuals of A. miyabei from 43 sites. Their genetic structure and diversity were analyzed using 12 microsatellite markers and cpDNA sequences.

RESULTS

According to structure analyses, ∆K was lowest at K = 2; the clustering essentially separated many of the individuals in the most northern regional group from the others. In contrast, the two southern groups were not clearly differentiated from each other, despite their geographic discontinuity. The proportion of private alleles was high in populations from the mountain terrain in the southern group although the number of extant populations is limited.

CONCLUSIONS

Genetic clustering of A. miyabei is not perfectly congruent with the current patterns of geographic distribution. We infer that disjunction of the two southern groups occurred more recently than that between these groups and the northern group. The mountainous landscape in the most southern region likely provided multiple refugia and contributed to the retention of distinctive genetic variation.

Genomic diversity and Demographic History of the Dromiciops genus (Marsupialia: Microbiotheriidae)

Three orders represent the South American fauna of marsupials. Of these, Microbiotheria was until recently known as a monotypic genus with the only surviving species Dromiciops gliroides (monito del monte). The recent proposal of a new Dromiciops species (Dromiciops bicinovici), together with new information on the origin and diversification of living microbioterians has changed the prevailing paradigm around the evolutionary history of these emblematic marsupials. Here, we used a RADseq approach to test for evidence of admixture and past or current gene flow among both species of Dromiciops and evaluate the genetic structure within D. gliroides. We analyzed 127 samples of Dromiciops distributed across the known distribution range of both species. We also inferred the joint demographic history of these lineages, thus corroborating the status of D. bozinovici as a distinct species. Demographic history reconstruction indicated that D. bozinovici diverged from D. gliroides around 4my ago and has remained isolated and demographically stable ever since. In contrast, D. gliroides is subdivided into three subclades that experienced recent expansions and moderate gene flow among them (mostly from north to south). Furthermore, genetic distances among populations within D. gliroides were significantly correlated with geographic distances. These results suggest that some of the D. gliroides populations would have survived in glacial refuges, with posterior expansions after ice retreat. Our results have important implications for the systematics of the genus and have profound conservation consequences for the new species, especially considering the fragmentation level of the temperate rainforest.

Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin

The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan Peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an “Out-of-Italy” expansion following the Messinian salinity crisis (∼5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian, and Balkan Peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flows have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.

The roles of dispersal limitation, climatic niches and glacial history in endemism of the North American bryophyte flora

PREMISE

Bryophytes (mosses, liverworts, and hornworts) tend to have very large geographic ranges, which impedes progress toward understanding the drivers of diversification and extinction. This study aimed to investigate whether North American endemics differ geographically from more widespread species and whether differences in climatic niche or traits related to dispersal and establishment differ between endemics and more widespread species.

METHODS

All available herbarium records of bryophytes from North America north of Mexico (10⁶ collections) were used. Traits related to dispersal were obtained from the literature. Analyses tested whether range sizes and extents differed between endemics and nonendemics, and whether trait differences were associated with endemism. Climate data were used to determine whether differences in niche breadth are present between endemics and nonendemics, and whether suitable climate for endemics occurs outside North America.

RESULTS

Nonendemics have range sizes twice as large as endemics and they occur farther north and have greater longitudinal extents. However, they do not have the widest niche breadths and do not differ in spore size (with few exceptions) or sexual condition. Asexual propagules are more prevalent among nonendemics. Climatic models indicate that substantial areas of climate suitable for endemics exist outside of North America.

CONCLUSIONS

Distributions of endemics and nonendemics are consistent with an important role of glaciation in shaping the North American bryophyte flora. Endemics are not limited to the continent based on a lack of suitable climate elsewhere or by spore size or sexual condition.

Pleistocene climate fluctuations as the major driver of genetic diversity and distribution patterns of the Caspian green lizard, Lacerta strigata Eichwald, 1831

Green lizards of the genus Lacerta have served as excellent models for studying the impact of Pleistocene climatic oscillations on genetic structures. The Caspian green lizard, Lacerta strigata, occupies various habitats across the Caucasus and the South Caspian Sea, with the Hyrcanian Forests and north of the Alborz Mountains forming the core of the range. This study aimed to re-examine the phylogenetic relationships of L. strigata with other congeneric members and to assess the genetic structure and historical demography of the species. Furthermore, Species Distribution Models (SDMs) were performed to infer the species' potential habitat suitability and were then projected on climate scenarios reflecting current and past (6 ky and 21 ky before present) conditions. A total of 39 individuals collected from most of the distribution range, together with additional lacertid species sequences from the GenBank database, were examined using mtDNA (Cyt b and 12S ribosomal RNA) and nuclear (C-mos and β-fibrinogen) sequence data. Based on the phylogenetic analyses, L. strigata was found to be a sister taxon to all other members of the genus. The species included two main clades (regional western and eastern) that diverged in a period between the Early and Middle Pleistocene. Based on the BBM and S-Diva analyses, both dispersal and vicariance events explained the phylogeographic structure of the species in the Hyrcanian Forests. The historical demographic analyses using Bayesian skyline plots showed a mild increase in the effective population size from about 120 Kya for the western regional clade. According to phylogeographic structures and SDMs evidence, as in other species within the region, it appears that the south of the Caspian Sea (Hyrcanian Forests), and the Alborz Mountains acted as multiple refugia during cold periods and promoted expansion outwards amid the warm periods. Overall, the results provided evidence that the genetic structure of the species has been influenced by the Pleistocene climatic fluctuations.

Evidence for ephemeral ring species formation during the diversification history of western fence lizards (Sceloporus occidentalis)

Divergence is often ephemeral, and populations that diverge in response to regional topographic and climatic factors may not remain reproductively isolated when they come into secondary contact. We investigated the geographical structure and evolutionary history of population divergence within Sceloporus occidentalis (western fence lizard), a habitat generalist with a broad distribution that spans the major biogeographical regions of Western North America. We used double digest RAD sequencing to infer population structure, phylogeny and demography. Population genetic structure is hierarchical and geographically structured with evidence for gene flow between biogeographical regions. Consistent with the isolation-expansion model of divergence during Quaternary glacial-interglacial cycles, gene flow and secondary contact are supported as important processes explaining the demographic histories of populations. Although populations may have diverged as they spread northward in a ring-like manner around the Sierra Nevada and southern Cascade Ranges, there is strong evidence for gene flow among populations at the northern terminus of the ring. We propose the concept of an "ephemeral ring species" and contrast S. occidentalis with the classic North American ring species, Ensatina eschscholtzii. Contrary to expectations of lower genetic diversity at northern latitudes following post-Quaternary-glaciation expansion, the ephemeral nature of divergence in S. occidentalis has produced centres of high genetic diversity for different reasons in the south (long-term stability) vs. the north (secondary contact).

Routes to global glaciation

Theory and observation suggest that Earth and Earth-like planets can undergo runaway low-latitude glaciation when changes in solar heating or in the carbon cycle exceed a critical threshold. Here, we use a simple dynamical-system representation of the ice-albedo feedback and the carbonate-silicate cycle to show that glaciation is also triggered when solar heating changes faster than a critical rate. Such 'rate-induced glaciations' remain accessible far from the outer edge of the habitable zone, because the warm climate state retains long-term stability. In contrast, glaciations induced by changes in the carbon cycle require the warm climate state to become unstable, constraining the kinds of perturbations that could have caused global glaciation in Earth's past. We show that glaciations can occur when Earth's climate transitions between two warm stable states; this property of the Earth system could help explain why major events in the development of life have been accompanied by glaciations.

Subglacial meltwater supported aerobic marine habitats during Snowball Earth

The Earth's most severe ice ages interrupted a crucial interval in eukaryotic evolution with widespread ice coverage during the Cryogenian Period (720 to 635 Ma). Aerobic eukaryotes must have survived the "Snowball Earth" glaciations, requiring the persistence of oxygenated marine habitats, yet evidence for these environments is lacking. We examine iron formations within globally distributed Cryogenian glacial successions to reconstruct the redox state of the synglacial oceans. Iron isotope ratios and cerium anomalies from a range of glaciomarine environments reveal pervasive anoxia in the ice-covered oceans but increasing oxidation with proximity to the ice shelf grounding line. We propose that the outwash of subglacial meltwater supplied oxygen to the synglacial oceans, creating glaciomarine oxygen oases. The confluence of oxygen-rich meltwater and iron-rich seawater may have provided sufficient energy to sustain chemosynthetic communities. These processes could have supplied the requisite oxygen and organic carbon source for the survival of early animals and other eukaryotic heterotrophs through these extreme glaciations.

Mountains as Evolutionary Arenas: Patterns, Emerging Approaches, Paradigm Shifts, and Their Implications for Plant Phylogeographic Research in the Tibeto-Himalayan Region

Recently, the "mountain-geobiodiversity hypothesis" (MGH) was proposed as a key concept for explaining the high levels of biodiversity found in mountain systems of the Tibeto-Himalayan region (THR), which comprises the Qinghai-Tibetan Plateau, the Himalayas, and the biodiversity hotspot known as the "Mountains of Southwest China" (Hengduan Mountains region). In addition to the MGH, which covers the entire life span of a mountain system, a complementary concept, the so-called "flickering connectivity system" (FCS), was recently proposed for the period of the Quaternary. The FCS focuses on connectivity dynamics in alpine ecosystems caused by the drastic climatic changes during the past ca. 2.6 million years, emphasizing that range fragmentation and allopatric speciation are not the sole factors for accelerated evolution of species richness and endemism in mountains. I here provide a review of the current state of knowledge concerning geological uplift, Quaternary glaciation, and the main phylogeographic patterns ("contraction/recolonization," "platform refugia/local expansion," and "microrefugia") of seed plant species in the THR. In addition, I make specific suggestions as to which factors future avenues of phylogeographic research should take into account based on the fundamentals presented by the MGH and FCS, and associated complementary paradigm shifts.

Abrupt global-ocean anoxia during the Late Ordovician-early Silurian detected using uranium isotopes of marine carbonates

The Late Ordovician mass extinction (LOME) terminated one of the greatest biodiversity radiations in Earth history eliminating ∼85% of marine animals, and it is coincident with the first major glaciation of the Phanerozoic. To evaluate LOME origins, we use uranium isotopes from marine limestones as a proxy for global-ocean redox conditions. Our results provide evidence of an abrupt global-ocean anoxic event coincident with the LOME onset and its continuation after the biologic recovery, through peak glaciation, and the following early Silurian deglaciation. These results also provide evidence for widespread ocean anoxia initiating and continuing during icehouse conditions.

Widespread marine anoxia is hypothesized as the trigger for the second pulse of the Late Ordovician (Hirnantian) mass extinction based on lithologic and geochemical proxies that record local bottom waters or porewaters. We test the anoxia hypothesis using δ²³⁸U values of marine limestones as a global seawater redox proxy. The δ²³⁸U trends at Anticosti Island, Canada, document an abrupt late Hirnantian ∼0.3‰ negative shift continuing through the early Silurian indicating more reducing seawater conditions. The lack of observed anoxic facies and no covariance among δ²³⁸U values and other local redox proxies suggests that the δ²³⁸U trends represent a global-ocean redox record. The Hirnantian ocean anoxic event (HOAE) onset is coincident with the extinction pulse indicating its importance in triggering it. Anoxia initiated during high sea levels before peak Hirnantian glaciation, and continued into the subsequent lowstand and early Silurian deglacial eustatic rise, implying that major climatic and eustatic changes had little effect on global-ocean redox conditions. The HOAE occurred during a global δ¹³C positive excursion, but lasted longer indicating that controls on the C budget were partially decoupled from global-ocean redox trends. U cycle modeling suggests that there was a ∼15% increase in anoxic seafloor area and ∼80% of seawater U was sequestered into anoxic sediments during the HOAE. Unlike other ocean anoxic events (OAE), the HOAE occurred during peak and waning icehouse conditions rather than during greenhouse climates. We interpret that anoxia was driven by global cooling, which reorganized thermohaline circulation, decreased deep-ocean ventilation, enhanced nutrient fluxes, stimulated productivity, which lead to expanded oxygen minimum zones.

Pleistocene glaciation of Fenland, England, and its implications for evolution of the region

Detailed investigation of landforms and their underlying deposits on the eastern margin of Fenland, East Anglia, demonstrated that they represent a series of glaciofluvial delta-fan and related sediments. Associated with these deposits are glacially dislocated sediments including tills, meltwater and pre-existing fluvial sediments. These 'Skertchly Line' deposits occur in the context of a substantial ice lobe that entered Fenland from the N to NE, dammed the streams entering the basin and caused glacial lakes to form in the valleys on the margins. Bulldozing by the ice lobe caused a series of ice-pushed ridges to form at the dynamic margin, especially at the ice maximum and during its retreat phases. Meltwater formed a series of marginal fans that coalesced into marginal accumulations in the SE of the basin. The ice lobe is named the Tottenhill glaciation. Further investigations of the Fenland margin have revealed the extent of the Tottenhill glaciation in the Fenland Basin, to the south and west, in sufficient detail to demonstrate the nature of the Tottenhill ice lobe and the landscape left on deglaciation. The ice lobe is likely to have been prone to surging. This is indicated by the low gradient of the ice lobe, the presence of underlying ductile Mesozoic clays, the evidence of ice-marginal flooding and the presence of arcuate glaciotectonic push moraines. Regional correlation, supported by independent numerical geochronology, indicates that the glaciation occurred ca 160 ka, i.e. during the late Middle Pleistocene, Marine Isotope Stage (MIS) 6, the Wolstonian Stage. Comparison and correlation across the southern North Sea Basin confirms that the glaciation is the equivalent of that during the Late Saalian Drenthe Stadial in The Netherlands. The implications of this correlation are presented. Before the glaciation occurred, the Fenland Basin did not exist. It appears to have been initiated by a subglacial tunnel valley system beneath the Anglian (=Elsterian, MIS 12) ice sheet. During the subsequent Hoxnian (=Holsteinian; approx. MIS 11) interglacial, the sea invaded the drainage system inherited following the glacial retreat. The evolution through the subsequent ca 200 ka Early to Middle Wolstonian substages, the interval between the Hoxnian (Holsteinian) temperate Stage and the Wolstonian glaciation, represents a period during which fluvial and periglacial activity modified the landscape under cold climates, and organic sediments were laid down during a warmer event. Palaeolithic humans were also periodically present during this interval, their artefacts having been reworked by the subsequent glaciation. The deglaciation was followed by re-establishment of the rivers associated with the deposition of Late Wolstonian (Warthe Stadial) gravels and sands, and later, deposits of the Ipswichian interglacial (=Eemian, approx. MIS 5e) including freshwater, then estuarine sediments. Subsequent evolution of the basin occurred during the Devensian Stage (=Weichselian, MIS 5d-2) under predominantly cold, periglacial conditions.

Evolutionary lessons from California plant phylogeography

Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures-both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change.

Formation of most of our coal brought Earth close to global glaciation

The bulk of Earth's coal deposits used as fossil fuel today was formed from plant debris during the late Carboniferous and early Permian periods. The high burial rate of organic carbon correlates with a significant drawdown of atmospheric carbon dioxide (CO₂) at that time. A recent analysis of a high-resolution record reveals large orbitally driven variations in atmospheric CO₂ concentration between [Formula: see text]150 and 700 ppm for the latest Carboniferous and very low values of 100 [Formula: see text] 80 ppm for the earliest Permian. Here, I explore the sensitivity of the climate around the Carboniferous/Permian boundary to changes in Earth's orbital parameters and in atmospheric CO₂ using a coupled climate model. The coldest orbital configurations are characterized by large axial tilt and small eccentricities of Earth's elliptical orbit, whereas the warmest configuration occurs at minimum tilt, maximum eccentricity, and a perihelion passage during Northern hemisphere spring. Global glaciation occurs at CO₂ concentrations <40 ppm, suggesting a rather narrow escape from a fully glaciated Snowball Earth state given the low levels and large fluctuations of atmospheric CO₂ These findings highlight the importance of orbital cycles for the climate and carbon cycle during the late Paleozoic ice age and the climatic significance of the fossil carbon stored in Earth's coal deposits.

Glacial weathering, sulfide oxidation, and global carbon cycle feedbacks

Connections between glaciation, chemical weathering, and the global carbon cycle could steer the evolution of global climate over geologic time, but even the directionality of feedbacks in this system remain to be resolved. Here, we assemble a compilation of hydrochemical data from glacierized catchments, use this data to evaluate the dominant chemical reactions associated with glacial weathering, and explore the implications for long-term geochemical cycles. Weathering yields from catchments in our compilation are higher than the global average, which results, in part, from higher runoff in glaciated catchments. Our analysis supports the theory that glacial weathering is characterized predominantly by weathering of trace sulfide and carbonate minerals. To evaluate the effects of glacial weathering on atmospheric pCO2, we use a solute mixing model to predict the ratio of alkalinity to dissolved inorganic carbon (DIC) generated by weathering reactions. Compared with nonglacial weathering, glacial weathering is more likely to yield alkalinity/DIC ratios less than 1, suggesting that enhanced sulfide oxidation as a result of glaciation may act as a source of CO2 to the atmosphere. Back-of-the-envelope calculations indicate that oxidative fluxes could change ocean-atmosphere CO2 equilibrium by 25 ppm or more over 10 ky. Over longer timescales, CO2 release could act as a negative feedback, limiting progress of glaciation, dependent on lithology and the concentration of atmospheric O2 Future work on glaciation-weathering-carbon cycle feedbacks should consider weathering of trace sulfide minerals in addition to silicate minerals.

Genetic assessment of the effects of streamscape succession on coho salmon Oncorhynchus kisutch colonization in recently deglaciated streams

Measures of genetic diversity within and among populations and historical geomorphological data on stream landscapes were used in model simulations based on approximate Bayesian computation (ABC) to examine hypotheses of the relative importance of stream features (geomorphology and age) associated with colonization events and gene flow for coho salmon Oncorhynchus kisutch breeding in recently deglaciated streams (50-240 years b.p.) in Glacier Bay National Park (GBNP), Alaska. Population estimates of genetic diversity including heterozygosity and allelic richness declined significantly and monotonically from the oldest and largest to youngest and smallest GBNP streams. Interpopulation variance in allele frequency increased with increasing distance between streams (r = 0·435, P < 0·01) and was inversely related to stream age (r = -0·281, P < 0·01). The most supported model of colonization involved ongoing or recent (<10 generations before sampling) colonization originating from large populations outside Glacier Bay proper into all other GBNP streams sampled. Results here show that sustained gene flow from large source populations is important to recently established O. kisutch metapopulations. Studies that document how genetic and demographic characteristics of newly founded populations vary associated with successional changes in stream habitat are of particular importance to and have significant implications for, restoration of declining or repatriation of extirpated populations in other regions of the species' native range.

Phenotypic plasticity of nest timing in a post-glacial landscape: how do reptiles adapt to seasonal time constraints?

Life histories evolve in response to constraints on the time available for growth and development. Nesting date and its plasticity in response to spring temperature may therefore be important components of fitness in oviparous ectotherms near their northern range limit, as reproducing early provides more time for embryos to complete development before winter. We used data collected over several decades to compare air temperature and nest date plasticity in populations of painted turtles and snapping turtles from a relatively warm environment (southeastern Michigan) near the southern extent of the last glacial maximum to a relatively cool environment (central Ontario) near the northern extent of post-glacial recolonization. For painted turtles, population-level differences in reaction norm elevation for two phenological traits were consistent with adaptation to time constraints, but no differences in reaction norm slopes were observed. For snapping turtle populations, the difference in reaction norm elevation for a single phenological trait was in the opposite direction of what was expected under adaptation to time constraints, and no difference in reaction norm slope was observed. Finally, among-individual variation in individual plasticity for nesting date was detected only in the northern population of snapping turtles, suggesting that reaction norms are less canalized in this northern population. Overall, we observed evidence of phenological adaptation, and possibly maladaptation, to time constraints in long-lived reptiles. Where present, (mal)adaptation occurred by virtue of differences in reaction norm elevation, not reaction norm slope. Glacial history, generation time, and genetic constraint may all play an important role in the evolution of phenological timing and its plasticity in long-lived reptiles.

Explosive ice age diversification of kiwi

Molecular dating largely overturned the paradigm that global cooling during recent Pleistocene glacial cycles resulted in a burst of species diversification although some evidence exists that speciation was commonly promoted in habitats near the expanding and retracting ice sheets. Here, we used a genome-wide dataset of more than half a million base pairs of DNA to test for a glacially induced burst of diversification in kiwi, an avian family distributed within several hundred kilometers of the expanding and retracting glaciers of the Southern Alps of New Zealand. By sampling across the geographic range of the five kiwi species, we discovered many cryptic lineages, bringing the total number of kiwi taxa that currently exist to 11 and the number that existed just before human arrival to 16 or 17. We found that 80% of kiwi diversification events date to the major glacial advances of the Middle and Late Pleistocene. During this period, New Zealand was repeatedly fragmented by glaciers into a series of refugia, with the tiny geographic ranges of many kiwi lineages currently distributed in areas adjacent to these refugia. Estimates of effective population size through time show a dramatic bottleneck during the last glacial cycle in all but one kiwi lineage, as expected if kiwi were isolated in glacially induced refugia. Our results support a fivefold increase in diversification rates during key glacial periods, comparable with levels observed in classic adaptive radiations, and confirm that at least some lineages distributed near glaciated regions underwent rapid ice age diversification.

Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges

Deterministic processes may uniquely affect codistributed species' phylogeographic patterns such that discordant genetic variation among taxa is predicted. Yet, explicitly testing expectations of genomic discordance in a statistical framework remains challenging. Here, we construct spatially and temporally dynamic models to investigate the hypothesized effect of microhabitat preferences on the permeability of glaciated regions to gene flow in two closely related montane species. Utilizing environmental niche models from the Last Glacial Maximum and the present to inform demographic models of changes in habitat suitability over time, we evaluate the relative probabilities of two alternative models using approximate Bayesian computation (ABC) in which glaciated regions are either (i) permeable or (ii) a barrier to gene flow. Results based on the fit of the empirical data to data sets simulated using a spatially explicit coalescent under alternative models indicate that genomic data are consistent with predictions about the hypothesized role of microhabitat in generating discordant patterns of genetic variation among the taxa. Specifically, a model in which glaciated areas acted as a barrier was much more probable based on patterns of genomic variation in Carex nova, a wet-adapted species. However, in the dry-adapted Carex chalciolepis, the permeable model was more probable, although the difference in the support of the models was small. This work highlights how statistical inferences can be used to distinguish deterministic processes that are expected to result in discordant genomic patterns among species, including species-specific responses to climate change.

Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae

PREMISE OF THE STUDY

Relationships among closely related and recently diverged taxa can be especially difficult to resolve. Here we use both Sanger sequencing and next-generation RADseq data sets to estimate phylogenetic relationships among species of Carex section Racemosae (Cyperaceae), a clade largely restricted to high latitudes and elevations. Interest in relationships among these taxa derives from questions about the species' biogeographic histories and possible links between diversification and Pleistocene glaciations.

METHODS

A combination of approaches and molecular markers were used to estimate relationships among Carex species within sect. Racemosae and taxa from closely related sections. Nuclear and chloroplast loci generated by Sanger sequencing were analyzed with *BEAST, and SNP data from RADseq loci were analyzed as a concatenated data set using maximum likelihood and as independent loci using SVDquartets.

KEY RESULTS

Sanger sequencing data sets resolved relationships among taxa at intermediate phylogenetic depths (albeit with low levels of support). Only the RADseq data resolved relationships with strong support at all phylogenetic depths. Moreover, different methods and data partitions of the RADseq data resulted in nearly identical topologies. Carex sect. Racemosae is a strongly supported clade, although a handful of species were found to group with closely related sections. Herbarium specimens up to 35 yr old successfully produced informative RADseq data.

CONCLUSIONS

Despite the short read lengths of RADseq data, they nevertheless resolved relationships that Sanger sequencing data did not. Resolution of the phylogenetic relationships among recently and rapidly diversifying taxa within sect. Racemosae clades suggest a role for the Pleistocene glaciations in clade diversification.

Comparative phylogeography and evolutionary history of schizothoracine fishes in the Changtang Plateau and their implications for the lake level and Pleistocene climate fluctuations

The water level oscillation of endorheic lakes and extent change of glaciers associated with the Asian monsoon are known as prominent representatives of climatic and environmental events in the Tibetan Plateau during the Quaternary. However, details process in spatial and temporal changes are still debated. We use the schizothoracines as a palaeoclimatic proxy to test two hypotheses concerning the evolution of Quaternary glaciations and lakes of the Changtang Plateau: (1) the Tibetan glaciations generally tended to decrease since the middle Pleistocene; (2) the lakes expansion was driven by summer monsoon rainfall. Based on a wide range‐wide sampling throughout in the Changtang Plateau and its adjacent drainages, we constructed phylogeny and demographic histories of schizothoracines in the Changtang Plateau. Our results showed that the populations of the exorheic rivers and lakes in southern Tibet possessed higher genetic variability, earlier coalescent and expansion times than those of the endorheic lakes in the Changtang Plateau. Population expansions are highly consistent with phases of strong summer monsoon and high lake level during interglacial stages. The maximum growth rate intervals showed three pulses from 64.7 to 54.8, 39.6 to 31.0, and 14.9 to 2.4 kya respectively. The significant positive correlations were found between regional precipitation and genetic diversity, as well as coalescence time of populations in the endorheic lakes. We suggested that the demographic history of the schizothoracines reflects the spatial and temporal changes in climate and lake level, in particular, in regional precipitation gradients associated with changes of the South Asian monsoon, and supports the climatic hypothesis of a general diminishing tend in Tibetan glaciations in the Tibetan Plateau since the middle Pleistocene.

Glaciated valleys in Europe and western Asia

In recent years, remote sensing, morphometric analysis, and other computational concepts and tools have invigorated the field of geomorphological mapping. Automated interpretation of digital terrain data based on impartial rules holds substantial promise for large dataset processing and objective landscape classification. However, the geomorphological realm presents tremendous complexity and challenges in the translation of qualitative descriptions into geomorphometric semantics. Here, the simple, conventional distinction of V-shaped fluvial and U-shaped glacial valleys was analyzed quantitatively using multi-scale curvature and a novel morphometric variable termed Difference of Minimum Curvature (DMC). We used this automated terrain analysis approach to produce a raster map at a scale of 1:6,000,000 showing the distribution of glaciated valleys across Europe and western Asia. The data set has a cell size of 3 arc seconds and consists of more than 40 billion grid cells. Glaciated U-shaped valleys commonly associated with erosion by warm-based glaciers are abundant in the alpine regions of mid Europe and western Asia but also occur at the margins of mountain ice sheets in Scandinavia. The high-level correspondence with field mapping and the fully transferable semantics validate this approach for automated analysis of yet unexplored terrain around the globe and qualify for potential applications on other planetary bodies like Mars.

Evolutionary history of Pacific salmon in dynamic environments

Contemporary evolution of Pacific salmon (Oncorhynchus spp.) is best viewed in the context of the evolutionary history of the species and the dynamic ecosystems they inhabit. Speciation was complete by the late Miocene, leaving c. six million years for intraspecific diversification. Following the most recent glacial maximum, large areas became available for recolonization. Current intraspecific diversity is thus the product of recent evolution overlaid onto divergent historical lineages forged during recurrent episodes of Pleistocene glaciation. In northwestern North America, dominant habitat features have been relatively stable for the past 5000 years, but salmon ecosystems remain dynamic because of disturbance regimes (volcanic eruptions, landslides, wildfires, floods, variations in marine and freshwater productivity) that occur on a variety of temporal and spatial scales. These disturbances both create selective pressures for adaptive responses by salmon and inhibit long-term divergence by periodically extirpating local populations and creating episodic dispersal events that erode emerging differences. Recent anthropogenic changes are replicated pervasively across the landscape and interrupt processes that allow natural habitat recovery. If anthropogenic changes can be shaped to produce disturbance regimes that more closely mimic (in both space and time) those under which the species evolved, Pacific salmon should be well-equipped to deal with future challenges, just as they have throughout their evolutionary history.

Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau

A knowledge of intraspecific divergence and range dynamics of dominant forest trees in response to past geological and climate change is of major importance to an understanding of their recent evolution and demography. Such knowledge is informative of how forests were affected by environmental factors in the past and may provide pointers to their response to future environmental change. However, genetic signatures of such historical events are often weak at individual loci due to large effective population sizes and long generation times of forest trees. This problem can be overcome by analysing genetic variation across multiple loci. We used this approach to examine intraspecific divergence and past range dynamics in the conifer Picea likiangensis, a dominant tree of forests occurring in eastern and southern areas of the Qinghai-Tibet Plateau (QTP). We sequenced 13 nuclear loci, two mitochondrial DNA regions and three plastid (chloroplast) DNA regions in 177 individuals sampled from 22 natural populations of this species, and tested the hypothesis that its evolutionary history was markedly affected by Pliocene QTP uplifts and Quaternary climatic oscillations. Consistent with the taxonomic delimitation of the three morphologically divergent varieties examined, all individuals clustered into three genetic groups with intervariety admixture detected in regions of geographical overlap. Divergence between varieties was estimated to have occurred within the Pliocene and ecological niche modelling based on 20 ecological variables suggested that niche differentiation was high. Furthermore, modelling of population-genetic data indicated that two of the varieties (var. rubescens and var. linzhiensis) expanded their population sizes after the largest Quaternary glaciation in the QTP, while expansion of the third variety (var. likiangensis) began prior to this, probably following the Pliocene QTP uplift. These findings point to the importance of geological and climatic changes during the Pliocene and Pleistocene as causes of intraspecific diversification and range shifts of dominant tree species in the QTP biodiversity hot spot region.

High-throughput SNP-genotyping analysis of the relationships among Ponto-Caspian sturgeon species

Legally certified sturgeon fisheries require population protection and conservation methods, including DNA tests to identify the source of valuable sturgeon roe. However, the available genetic data are insufficient to distinguish between different sturgeon populations, and are even unable to distinguish between some species. We performed high-throughput single-nucleotide polymorphism (SNP)-genotyping analysis on different populations of Russian (Acipenser gueldenstaedtii), Persian (A. persicus), and Siberian (A. baerii) sturgeon species from the Caspian Sea region (Volga and Ural Rivers), the Azov Sea, and two Siberian rivers. We found that Russian sturgeons from the Volga and Ural Rivers were essentially indistinguishable, but they differed from Russian sturgeons in the Azov Sea, and from Persian and Siberian sturgeons. We identified eight SNPs that were sufficient to distinguish these sturgeon populations with 80% confidence, and allowed the development of markers to distinguish sturgeon species. Finally, on the basis of our SNP data, we propose that the A. baerii-like mitochondrial DNA found in some Russian sturgeons from the Caspian Sea arose via an introgression event during the Pleistocene glaciation.

In the present study, the high-throughput genotyping analysis of several sturgeon populations was performed. SNP markers for species identification were defined. The possible explanation of the baerii-like mitotype presence in some Russian sturgeons in the Caspian Sea was suggested.

Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)

Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ∼13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.

Origin and provenance of spherules and magnetic grains at the Younger Dryas boundary

One or more bolide impacts are hypothesized to have triggered the Younger Dryas cooling at ∼12.9 ka. In support of this hypothesis, varying peak abundances of magnetic grains with iridium and magnetic microspherules have been reported at the Younger Dryas boundary (YDB). We show that bulk sediment and/or magnetic grains/microspherules collected from the YDB sites in Arizona, Michigan, New Mexico, New Jersey, and Ohio have (187)Os/(188)Os ratios ≥1.0, similar to average upper continental crust (= 1.3), indicating a terrestrial origin of osmium (Os) in these samples. In contrast, bulk sediments from YDB sites in Belgium and Pennsylvania exhibit (187)Os/(188)Os ratios <<1.0 and at face value suggest mixing with extraterrestrial Os with (187)Os/(188)Os of ∼0.13. However, the Os concentration in bulk sample and magnetic grains from Belgium is 2.8 pg/g and 15 pg/g, respectively, much lower than that in average upper continental crust (=31 pg/g), indicating no meteoritic contribution. The YDB site in Pennsylvania is remarkable in yielding 2- to 5-mm diameter spherules containing minerals such as suessite (Fe-Ni silicide) that form at temperatures in excess of 2000 °C. Gross texture, mineralogy, and age of the spherules appear consistent with their formation as ejecta from an impact 12.9 ka ago. The (187)Os/(188)Os ratios of the spherules and their leachates are often low, but Os in these objects is likely terrestrially derived. The rare earth element patterns and Sr and Nd isotopes of the spherules indicate that their source lies in 1.5-Ga Quebecia terrain in the Grenville Province of northeastern North America.

Phylogeography of sea oats (Uniola paniculata), a dune-building coastal grass in southeastern North America

We tested the hypothesis that Uniola paniculata populations are divided into eastern and western lineages, with the primary geographic break at the southern tip of Florida, as observed in codistributed animal taxa. We asked whether the geographic distribution of chloroplast DNA (cpDNA) variation in U. paniculata corresponds to 1) genetic structure in nuclear variation reported in previous studies, and 2) the geographic distribution of morphological adaptive traits reported in previous studies. We sampled 66 populations and performed phylogeographic analyses using sequence variations in maternally inherited cpDNA. We reconstructed the intraspecific phylogenetic network with TCS software and identified phylogeographic breaks in the species using Monmonier's algorithm. Analyses identified 6 cpDNA haplotypes and 2 major lineages: eastern (Atlantic) and western (Gulf), with a phylogeographic break at the southern tip of Florida. The data suggest U. paniculata survived the last glacial maximum (LGM) in southern refugia. Following the LGM, differential leading-edge recolonization explains the current distribution of haplotypes into 2 lineages. Populations containing a haplotype from outside its native range are likely due to human-mediated transplantation. The genetic structure of cpDNA variation has weak correlation with nuclear DNA variation, and there is partial concordance between the geographic distribution of cpDNA and morphological variation.

Diversity and endemism in deglaciated areas: ploidy, relative genome size and niche differentiation in the Galium pusillum complex (Rubiaceae) in Northern and Central Europe

BACKGROUND AND AIMS

Plants endemic to areas covered by ice sheets during the last glaciation represent paradigmatic examples of rapid speciation in changing environments, yet very few systems outside the harsh arctic zone have been comprehensively investigated so far. The Galium pusillum aggregate (Rubiaceae) is a challenging species complex that exhibits a marked differentiation in boreal parts of Northern Europe. As a first step towards understanding its evolutionary history in deglaciated regions, this study assesses cytological variation and ecological preferences of the northern endemics and compares the results with corresponding data for species occurring in neighbouring unglaciated parts of Central and Western Europe.

METHODS

DNA flow cytometry was used together with confirmatory chromosome counts to determine ploidy levels and relative genome sizes in 1158 individuals from 181 populations. A formalized analysis of habitat preferences was applied to explore niche differentiation among species and ploidy levels.

KEY RESULTS

The G. pusillum complex evolved at diploid and tetraploid levels in Northern Europe, in contrast to the high-polyploid evolution of most other northern endemics. A high level of eco-geographic segregation was observed between different species (particularly along gradients of soil pH and competition) which is unusual for plants in deglaciated areas and most probably contributes to maintaining species integrity. Relative monoploid DNA contents of the species from previously glaciated regions were significantly lower than those of their counterparts from mostly unglaciated Central Europe, suggesting independent evolutionary histories.

CONCLUSIONS

The aggregate of G. pusillum in Northern Europe represents an exceptional case with a geographically vicariant and ecologically distinct diploid/tetraploid species endemic to formerly glaciated areas. The high level of interspecific differentiation substantially widens our perception of the evolutionary dynamics and speciation rates in the dramatically changing environments of Northern Europe.

Deglaciation explains bat extinction in the Caribbean

Ecological factors such as changing climate on land and interspecific competition have been debated as possible causes of postglacial Caribbean extinction. These hypotheses, however, have not been tested against a null model of climate-driven postglacial area loss. Here, we use a new Quaternary mammal database and deep-sea bathymetry to estimate species-area relationships (SARs) at present and during the Last Glacial Maximum (LGM) for bats of the Caribbean, and to model species loss as a function of area loss from rising sea level. Island area was a significant predictor of species richness in the Bahamas, Greater Antilles, and Lesser Antilles at all time periods, except for the Lesser Antilles during the LGM. Parameters of LGM and current SARs were similar in the Bahamas and Greater Antilles, but not the Lesser Antilles, which had fewer estimated species during the LGM than expected given their size. Estimated postglacial species losses in the Bahamas and Greater Antilles were largely explained by inferred area loss from rising sea level in the Holocene. However, there were more species in the Bahamas at present, and fewer species in the smaller Greater Antilles, than expected given island size and the end-Pleistocene/early Holocene SARs. Poor fossil sampling and ecological factors may explain these departures from the null. Our analyses illustrate the importance of changes in area in explaining patterns of species richness through time and emphasize the role of the SAR as a null hypothesis in explorations of the impact of novel ecological interactions on extinction.