Evolutionary history of alpine and subalpine Daphnia in western North America

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Measuring microbial fitness in a field reciprocal transplant experiment

Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to different habitats or locations. We designed a competitive fitness assay to detect adaptation of Saccharomyces paradoxus isolates to the habitat they were isolated from (oak or larch leaf litter). The assay accurately measures relative fitness by tracking genotype frequency changes in the field using digital droplet PCR (DDPCR). We expected locally adapted S. paradoxus strains to increase in frequency over time when growing on the leaf litter type from which they were isolated. The DDPCR assay successfully detected fitness differences among S. paradoxus strains, but did not find a tendency for strains to be adapted to the habitat they were isolated from. Instead, we found that the natural alleles of the hexose transport gene we used to distinguish S. paradoxus strains had significant effects on fitness. The origin of a strain also affected its fitness: strains isolated from oak litter were generally fitter than strains from larch litter. Our results suggest that dispersal limitation and genetic drift shape S. paradoxus populations in the forest more than local selection does, although further research is needed to confirm this. Tracking genotype frequency changes using DDPCR is a practical and accurate microbial fitness assay for natural environments.     

Evolutionary diversification of cryophilic <Emphasis Type="Italic">Grylloblatta</Emphasis>species (Grylloblattodea: Grylloblattidae) in alpine habitats of California

Background  

Climate in alpine habitats has undergone extreme variation during Pliocene and Pleistocene epochs, resulting in repeated expansion and contraction of alpine glaciers. Many cold-adapted alpine species have responded to these climatic changes with long-distance range shifts. These species typically exhibit shallow genetic differentiation over a large geographical area. In contrast, poorly dispersing organisms often form species complexes within mountain ranges, such as the California endemic ice-crawlers (Grylloblattodea: Grylloblattidae: Grylloblatta). The diversification pattern of poorly dispersing species might provide more information on the localized effects of historical climate change, the importance of particular climatic events, as well as the history of dispersal. Here we use multi-locus genetic data to examine the phylogenetic relationships and geographic pattern of diversification in California Grylloblatta.     

Host and geography together drive early adaptive radiation of Hawaiian planthoppers

The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects “escape and radiate” on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host in structuring populations in the early stages of differentiation on the youngest islands of the Hawaiian chain. Results from extensive exon capture data showed that N. umbratica is highly structured, both by geography, with discrete populations on each volcano, and by host plant, with parallel radiations on Clermontia and Pipturus leading to extensive co‐occurrence. The marked genetic structure suggests that populations can readily become established on novel hosts provided opportunity; subsequent adaptation allows monopolization of the new host. The results support the role of geographic isolation in structuring populations and with host shifts occurring as discrete events that facilitate subsequent parallel geographic range expansion.     

Identification of ungulates used in a traditional Chinese medicine with DNA barcoding technology

Horns of Saiga antelope (Saiga tatarica) have always been an ingredient of “Lingyangjiao”, a traditional Chinese medicine (TCM). Persistent hunting for Saiga antelope has already threatened the survival of critical endangered populations in wild. To control the growing pressure, CITES and Chinese government have legislated for monitoring the trade of Saiga horns. However, similar ungulate horns are difficult to identify by their morphological characteristics, which has impeded the law enforcement. Besides Saiga antelope, other seven ungulate species which have similar horns are also sold and marked as “Lingyangjiao” in TCM markets to offset shortage of Saiga antelope horns. Such species are Gazella subgutturosa, Pantholops hodgsonii, Procapra picticaudata, Procapra gutturosa, Procapra przewalskii, Capra hircus, and Ovis aries. Our study aimed at implementing DNA barcoding technology to diagnose Saiga horns and the substitutes. We successfully extracted genomic DNA from horn samples. We recovered COI sequences of 644 bp with specific primers and 349 bp with nested PCR primers designed for degraded horn samples. The mean interspecific genetic distance of data set of the 644‐bp full barcodes and the 349‐bp mini‐barcodes was 14.96% and 15.38%, respectively, and the mean intraspecific distance was 0.24% and 0.20%, respectively. Each species formed independent clades in neighbor‐joining (NJ) phylogenetic tree of the two data sets with >99% supporting values, except P. gutturosa and P. przewalskii. The deep genetic distances gap and clear species clades in NJ tree of either full barcodes or mini‐barcodes suggest that barcoding technology is an effective tool to diagnose Saiga horns and their substitutes. Barcoding diagnosis protocol developed here will simplify diagnosis of “Lingyangjiao” species and will facilitate conservation of endangered ungulates involved in TCM “Lingyangjiao” markets, especially the Saiga antelope.     

Selective predation on the broad‐toothed rat,Mastacomys fuscus (Rodentia: Muridae), by the introduced red fox,Vulpes vulpes (Carnivora: Canidae), in the Snowy Mountains,Australia

Abstract Since 1981 there has been debate over whether foxes (Vulpes vulpes Linnaeus) selectively prey on the broad‐toothed rat (Mastacomys fuscus Thomas) relative to the bush rat (Rattus fuscipes (Waterhouse)). In the present study, three areas of the argument are examined. (i) In a study of fox diet over 3 years at both alpine and subalpine altitudes, M. fuscus outnumbered R. fuscipes in faecal remains in all seasons, in all years, and at both altitudes. Overall, M. fuscus occurred in scats five times as frequently as did R. fuscipes in the alpine zone and twice as often in the subalpine zone. (ii) Data from population studies of M. fuscus and R. fuscipes showed no evidence that M. fuscus is trap shy; neither the pattern of captures of individuals caught once, twice and so on, nor the proportion of the estimated population of each species captured during trapping sessions was significantly different. (iii) The suitable habitat for M. fuscus within the potential home ranges of foxes contributing to the subalpine fox scat collection constituted approximately 50% of the total area. However, there was no significant difference between the numbers of fox trails encountered in habitat suitable or unsuitable for M. fuscus in 19 paired transects skied in winter, indicating no preferential foraging in either habitat. Selective feeding on M. fuscus was therefore established, but how that choice is exercised was not determined.     

Climate‐induced glacier and snow loss imperils alpine stream insects

Climate warming is causing rapid loss of glaciers and snowpack in mountainous regions worldwide. These changes are predicted to negatively impact the habitats of many range‐restricted species, particularly endemic, mountaintop species dependent on the unique thermal and hydrologic conditions found only in glacier‐fed and snow melt‐driven alpine streams. Although progress has been made, existing understanding of the status, distribution, and ecology of alpine aquatic species, particularly in North America, is lacking, thereby hindering conservation and management programs. Two aquatic insects – the meltwater stonefly (Lednia tumana) and the glacier stonefly (Zapada glacier) – were recently proposed for listing under the U.S. Endangered Species Act due to climate‐change‐induced habitat loss. Using a large dataset (272 streams, 482 total sites) with high‐resolution climate and habitat information, we describe the distribution, status, and key environmental features that limit L. tumana and Z. glacier across the northern Rocky Mountains. Lednia tumana was detected in 113 streams (175 sites) within Glacier National Park (GNP) and surrounding areas. The probability of L. tumana occurrence increased with cold stream temperatures and close proximity to glaciers and permanent snowfields. Similarly, densities of L. tumana declined with increasing distance from stream source. Zapada glacier was only detected in 10 streams (24 sites), six in GNP and four in mountain ranges up to ~600 km southwest. Our results show that both L. tumana and Z. glacier inhabit an extremely narrow distribution, restricted to short sections of cold, alpine streams often below glaciers predicted to disappear over the next two decades. Climate warming‐induced glacier and snow loss clearly imperils the persistence of L. tumana and Z. glacier throughout their ranges, highlighting the role of mountaintop aquatic invertebrates as sentinels of climate change in mid‐latitude regions.     

The wing morphology of limnephilid caddisflies in relation to their habitat preferences

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Repeated evolution of terrestrial lineages in a continental lizard radiation

The “early‐burst” model of adaptive radiation predicts an early increase in phenotypic disparity concurrent with lineage diversification. Although most studies report a lack of this coupled pattern, the underlying processes are not identified. The continental radiation of Hemidactylus geckos from Peninsular India includes morphologically diverse species that occupy various microhabitats. This radiation began diversifying ~36 Mya with an early increase in lineage diversification. Here, we test the “early‐burst” hypothesis by investigating the presence of ecomorphs and examining the pattern of morphological diversification in a phylogenetic framework. Two ecomorphs—terrestrial and scansorial species—that vary significantly in body size and toepad size were identified. Unlike the prediction of the “early‐burst” model, we find that disparity in toepad morphology accumulated more recently ~14 Mya and fit the Ornstein‐Ulhenbeck model. Ancestral state reconstruction of the two ecomorphs demonstrates that terrestrial lineages evolved independently at least five times from scansorial ancestors, with the earliest diversification in terrestrial lineages 19–12 Mya. Our study demonstrates a delayed increase in morphological disparity as a result of the evolution of terrestrial ecomorphs. The diversification of terrestrial lineages is concurrent with the establishment of open habitat and grasslands in Peninsular India, suggesting that the appearance of this novel resource led to the adaptive diversification.     

Wettability and Contaminability of Insect Wings as a Function of Their Surface Sculptures

Abstract The wing surfaces of 97 insect species from virtually all relevant major groups were examined by high resolution scanning-electron-microscopy, in order to identify the relationships between the wing microstructures, their wettability with water and their behaviour under the influence of contamination. Isolated wings with contact angles between 31.6° and 155.5° were artificially contaminated with silicate dusts and subsequently fogged until drops of water (“dew”) formed and rolled off. The remaining particles were counted via a digital image analysis system. Remaining particle values between 0.41% and 103% were determined in comparison with unfogged controls. Some insects with very unwettable wings show a highly significant “self-cleaning” effect under the influence of rain or dew. Detailed analysis revealed that there is a correlation between the wettability and the “SM Index” (quotient of wing surface/(body mass)^0.67) with values ranging from 2.42 to 57.0. Furthermore, there is a correlation between the “self-cleaning” effect and the SM Index, meaning that taxa with a high SM Index, e.g. “large-winged” Ephemeroptera, Odonata, Planipennia, and many Lepidoptera, have very unwettable wings and show high particle removal due to dripping water drops. The “small-winged” insects, such as Diptera and Hymenoptera, and insects with elytra, such as Blattariae, Saltatoria, Heteroptera and Coleoptera, show completely opposite effects. This is clearly a result of the fact that species with a high SM Index are, in principle, more restricted in flight by contamination than species with a low SM Index which can also actively clean their own wings. The wings primarily serve a protection function in insects with elytra, so that the effects of contamination are probably of minor importance in these insects. Copyright © 1996 The Royal Swedish Academy of Sciences. Published by Elsevier Science Ltd.     

Staying in situ or shifting range under ongoing climate change: A case of an endemic herb in the Himalaya-Hengduan Mountains across elevational gradients

Aim

How species respond to ongoing climate change has been a hot research topic, especially with the controversy in shifting range (movement) or persisting in local habitat (in situ) as the primary response. Assessing the relative roles of range shifts, phenotypic plasticity and genetic adaptation helps us predict the evolutionary fate of species. We aim to explore the evolutionary strategies of plants under climate change from a keystone herb in alpine ecosystems, Mirabilis himalaica, along its elevational gradient.

Location

Himalaya-Hengduan Mountains, China.

Methods

We combined evidence from population genomics and ecological data in both space and time to investigate the state of “staying” or “moving”. We identified migration events by assessing historical and contemporary gene flow and changes in species distribution. Morphological variation was compared by measuring five traits using specimen data. Moreover, we explored climate-driven genetic variation and local selection regimes acting on populations in the alpine landscape along an elevational gradient.

Results

Our results argue that staying in situ by morphological variation and local genetic evolution rather than range shifting plays an important role in M. himalaica response to climate change. We first found trace evidence of upward or climatic-driven shifting along an elevational gradient, although asymmetric gene flow was restricted within microenvironments of mid-elevational populations. Furthermore, morphological variation comparisons revealed clinal variation, as resource allocation showed a declining pattern in vegetative growth but increased reproductive growth with increasing elevation. Outlier tests and environment association analyses indicated adaptative loci primarily related to thermal-driven selection and continuous adaptations to high elevation in the Himalaya-Hengduan Mountains.

Main Conclusions

Our findings show M. himalaica may persist in local habitats rather than shifting range under climate change, exhibiting a low risk of genomic vulnerability in current habitats. This study has important implications in improving our understanding of the evolutionary response in alpine plants to climate change.     

Long-term effects of grazing on subalpine and alpine grasslands in the Central Alps,Austria

The effects of grazing exclusion on species diversity and functional diversity were analyzed along an elevation gradient from the subalpine (1960 m a.s.l.) to the lower and upper alpine zone (2275 m–2650 m a.s.l.) in the Austrian Central Alps for 15 years. Nine sites were chosen, including grasslands at different elevations, a bog and a glacier foreland site at the lower alpine zone and a snowbed at the upper alpine zone. Data were acquired by frequency counts in 1 m² permanent plots inside each fenced area (three plots per site) and outside in grazed areas (three plots). Diversity indices and functional diversity were analyzed by means of generalized linear mixed models (GLMMs). Exclosure, duration of exclusion and exclosure*years (interaction effect) were defined as predictor variables. Multivariate ordination techniques were used to (i) determine species responses to grazing exclusion (pRDA, partial redundancy analysis) and (ii) to create a distance matrix representing the changes between exclosures and control plots per year (NMDS, non-metric multidimensional scaling). At the subalpine grassland, first differences between exclosure and control plots occurred already only after three years, at the upper alpine zone after four and five years. Contrary to our expectation, dwarf shrubs did not increase within the exclosures of the subalpine grassland. Instead, mainly the tall forb Geranium sylvaticum increased. Species richness significantly decreased at the exclosures of the subalpine zone, the snowbed and at one upper alpine grassland sites. The communities of the glacier foreland and the bog were hardly affected by grazing exclusion.We conclude that plant species and communities react individually depending on elevation and grazing animals. Grazing exclusion studies at high elevations should definitely be carried out in the long-term.     

Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification

Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G‐gene sequence variation, in comparison with whole‐genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G‐gene haplotypes from 2003 to 2017, stemming from two originals (“a” and “b”). G‐gene haplotypes “a” and “b” differed by just one synonymous single‐nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group “a” descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group “b” descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole‐genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G‐gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV‐IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.     

Spatio‐temporal genetic structure and the effects of long‐term fishing in two partially sympatric offshore demersal fishes

Environmental gradients have been shown to disrupt gene flow in marine species, yet their influence in structuring populations at depth remains poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis) are demersal species co‐occurring in the Benguela Current system, where decades of intense fishing resulted in severely depleted stocks in the past. Previous studies identified conflicting mtDNA genetic substructuring patterns and thus contrasting evolutionary trajectories for both species. Using 10 microsatellite loci, the control region of mtDNA and employing a seascape genetics approach, we investigated genetic connectivity and the impact of prolonged exploitation in the two species, which are characterized by different patterns of fishing pressure. Three consecutive years were sampled covering the entire distribution (N = 2100 fishes). Despite large estimated population sizes, both species exhibited low levels of contemporary genetic diversity (0.581 < H_E < 0.692), implying that fishing has had a significant impact on their genetic composition and evolutionary trajectories. Further, for M. paradoxus, significant temporal, but not spatial, divergence points to the presence of genetic chaotic patchiness. In contrast, M. capensis exhibited a clear latitudinal cline in genetic differentiation between Namibia and South Africa (F_ST = 0.063, P < 0.05), with low (0.2% per generation) estimates of contemporary gene flow. Seascape analyses reveal an association with bathymetry and upwelling events, suggesting that adaptation to local environmental conditions may drive genetic differentiation in M. capensis. Importantly, our results highlight the need for temporal sampling in disentangling the complex factors that impact population divergence in marine fishes.     

Phylogeographic patterns and species delimitation in the endangered silverside “humboldtianum” clade (Pisces: Atherinopsidae) in central Mexico: understanding their evolutionary history

The Atherinopsidae is the second largest group of freshwater fishes occupying central Mexico and is one of biological, cultural, and economic importance. The “humboldtianum” clade (Genus Chirostoma) is a “species flock” of nine described species that inhabit lacustrine ecosystems in central Mexico. The high morphological polymorphism within the group makes species identification difficult and thereby limits the development of research and management projects focusing on this group. In this study, we used phylogeographic and coalescent-based methods to understand the evolution of genetic variation among these species. The results revealed taxonomic inaccuracies and genetic admixture among species. Genetic variation was structured geographically, rather than taxonomically, and five closely related genetic groups were recovered. Two evolutionary pathways were found. First, a novel geographical arrangement of haplotypes was recovered that gave rise to the five recently (Pleistocene, <?1 Myr) derived genetic groups. The second pathway showed a recent intra-lacustrine genetic differentiation that could be associated with sympatric or ecological speciation. The current classification of the group is revised and includes a reduction in the number of valid species in the “humboldtianum” clade. Moreover, this study provides new insight into the biogeography and evolutionary history of this important group of fishes.

     

Seasonal changes in anthocyanin contents and in activities of xanthophyll and ascorbate–glutathione cycles in Sabina species derived from different environments

Qilian Juniper (Sabina przewalskii Kom.) and Chinese juniper [Sabina chinensis (Lin.) Ant.] are overwintering plants. S. przewalskii, a protected species in China, is distributed in subalpine and alpine area on the Qinghai-Tibet Plateau. S. chinensis is distributed in plain area. We investigated seasonal changes in photoprotective stress compounds such as anthocyanins, activities of three enzymes of ascorbate–glutathione pathway, as well as xanthophyll size and conversion in these species. Ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR) and glutathione reductase (GR) levels were higher in the low-temperature months, which was associated with changes in anthocyanins and in de-epoxidation index [(A + Z)/(V + A + Z)]. Photochemical efficiency of PSII (Fv/Fm) was lower (<0.70) during winter and late autumn in both species. During the low-temperature months, S. przewalskii had higher levels of photoprotective stress compounds than S. chinensis. The results suggested that these two species possess cold-induced photoinhibition functions and show the inherent, season-dependent differences in the amounts of the stress-related compounds.     

Experimental warming increases herbivory by leaf‐chewing insects in an alpine plant community

Climate warming is predicted to affect species and trophic interactions worldwide, and alpine ecosystems are expected to be especially sensitive to changes. In this study, we used two ongoing climate warming (open‐top chambers) experiments at Finse, southern Norway, to examine whether warming had an effect on herbivory by leaf‐chewing insects in an alpine Dryas heath community. We recorded feeding marks on the most common vascular plant species in warmed and control plots at two experimental sites at different elevations and carried out a brief inventory of insect herbivores. Experimental warming increased herbivory on Dryas octopetala and Bistorta vivipara. Dryas octopetala also experienced increased herbivory at the lower and warmer site, indicating an overall positive effect of warming, whereas B. vivipara experienced an increased herbivory at the colder and higher site indicating a mixed effect of warming. The Lepidoptera Zygaena exulans and Sympistis nigrita were the two most common leaf‐chewing insects in the Dryas heath. Based on the observed patterns of herbivory, the insects life cycles and feeding preferences, we argue that Z. exulans is the most important herbivore on B. vivipara, and S. nigrita the most important herbivore on D. octopetala. We conclude that if the degree of insect herbivory increases in a warmer world, as suggested by this study and others, complex interactions between plants, insects, and site‐specific conditions make it hard to predict overall effects on plant communities.