Closely-related Species Research Articles

Differential responses of the scavenging systems for reactive oxygen species (ROS) and reactive carbonyl species (RCS) to UV-B irradiation in Arabidopsis thaliana and its high altitude perennial relative Arabis alpina.

The present work aimed to compare antioxidant response and lipid peroxide detoxification capacity of an arctic-alpine species Arabis alpina to its close relative model species Arabidopsis thaliana under acute short duration (3h and 6h) UV-B stress (4.6 and 8.2W/m2). After 3 and 6h exposure to UV-B, A. alpina showed lower lipid peroxidation and H2O2 accumulation when compared to A. thaliana. Moreover, Fv/Fm value of A. thaliana dropped to 0.70, while A. alpina dropped to 0.75 indicating better protection of PSII in this species. For elucidation of the antioxidant response, activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POX), ascorbate peroxidase (APX), glutathione reductase (GR) and dehydroascorbate reductase (DHAR) were measured. SOD induction with 6h of UV-B was more prominent in A. alpina. Also, A. alpina had higher chloroplastic FeSOD activity when compared to A. thaliana. APX activity was also significantly induced in A. alpina, while its activity decreased at 3h or did not change at 6h in A. thaliana. A. alpina was able to maintain constant CAT activity, but drastic decreases were observed in A. thaliana at both time points. Moreover, A. alpina was able to maintain or induce aldehyde dehydrogenase (ALDH), alkenal reductases (AERs) and glutathione-S-transferases (GST) activity, while an opposite trend was observed in A. thaliana. These findings indicate that A. alpina was able to maintain/induce its antioxidant defence and lipid peroxide detoxification conferring better protection against UV-B.

The tyranny of phylogeny-A plea for a less dogmatic stance on two-species comparisons: Funding bodies, journals and referees discourage two- or few-species comparisons, but such studies provide essential insights complementary to phylogenetic comparative studies.

Phylogenetically controlled studies across multiple species correct for taxonomic confounds in physiological performance traits. Therefore, they are preferred over comparisons of two or few closely-related species. Funding bodies, referees and journal editors nowadays often even reject to consider detailed comparisons of two or few closely related species. Here, we plea for a less dogmatic stance on such comparisons, because phylogenetic studies come with their own limitations similar in magnitude as those of two-species comparisons. Two-species comparisons are particularly relevant and instructive for understanding physiological pathways and de novo mutations in three contexts: in a purely mechanistic context, when differences in the regulation of a trait are the focus of investigation, when a physiological trait lacks a direct connection to fitness, and when physiological measures cannot easily be standardized among laboratories. In conclusion, phylogenetic comparative and two-species studies have different strengths and weaknesses and combining these complementary approaches will help integrating biology.

Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species.

Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the tropics. Several laws and regulations have been set up to combat illegal timber trade. Despite significant enforcement efforts of these regulations, illegal logging continues to be a serious problem and impacts for the functioning of the forest ecosystem and global biodiversity in the tropics. Microscopic analysis of wood samples and the use of conventional plant DNA barcodes often do not allow to distinguish closely-related species. The use of novel molecular technologies could make an important contribution for the identification of tree species. In this study, we used high-throughput sequencing technologies and bioinformatics tools to obtain the complete de-novo chloroplast genome of 62 commercial African timber species using the genome skimming method. Then, we performed a comparative genomic analysis that revealed new candidate genetic regions for the discrimination of closely-related species. We concluded that genome skimming is a promising method for the development of plant genetic markers to combat illegal logging activities supporting CITES, FLEGT and the EU Timber Regulation.

Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille

BackgroundTracing the association between insect cold tolerance and latitudinally and locally varying environmental conditions, as well as key morphological traits and molecular mechanisms, is essential for understanding the processes involved in adaptation. We explored these issues in two closely-related species, Drosophila montana and Drosophila flavomontana, originating from diverse climatic locations across several latitudes on the coastal and mountainous regions of North America. We also investigated the association between sequence variation in one of the key circadian clock genes, vrille, and cold tolerance in both species. Finally, we studied the impact of vrille on fly cold tolerance and cold acclimation ability by silencing it with RNA interference in D. montana.ResultsWe performed a principal component analysis (PCA) on variables representing bioclimatic conditions on the study sites and used latitude as a proxy of photoperiod. PC1 separated the mountainous continental sites from the coastal ones based on temperature variability and precipitation, while PC2 arranged the sites based on summer and annual mean temperatures. Cold tolerance tests showed D. montana to be more cold-tolerant than D. flavomontana and chill coma resistance (CTmin) of this species showed an association with PC2. Chill coma recovery time (CCRT) of both species improved towards northern latitudes, and in D. flavomontana this trait was also associated with PC1. D. flavomontana flies were darkest in the coast and in the northern mountainous populations, but coloration showed no linkage with cold tolerance. Body size decreased towards cold environments in both species, but only within D. montana populations largest flies showed fastest recovery from cold. Finally, both the sequence analysis and RNAi study on vrille suggested this gene to play an essential role in D. montana cold resistance and acclimation, but not in recovery time.ConclusionsOur study demonstrates the complexity of insect cold tolerance and emphasizes the need to trace its association with multiple environmental variables and morphological traits to identify potential agents of natural selection. It also shows that a circadian clock gene vrille is essential both for short- and long-term cold acclimation, potentially elucidating the connection between circadian clock system and cold tolerance.

Interspecific and intraspecific foraging differentiation of neighbouring tropical seabirds

BackgroundSocial interactions, reproductive demands and intrinsic constraints all influence foraging decisions in animals. Understanding the relative importance of these factors in shaping the way that coexisting species within communities use and partition resources is central to knowledge of ecological and evolutionary processes. However, in marine environments, our understanding of the mechanisms that lead to and allow coexistence is limited, particularly in the tropics.MethodsUsing simultaneous data from a suite of animal-borne data loggers (GPS, depth recorders, immersion and video), dietary samples and stable isotopes, we investigated interspecific and intraspecific differences in foraging of two closely-related seabird species (the red-footed booby and brown booby) from neighbouring colonies on the Cayman Islands in the Caribbean.ResultsThe two species employed notably different foraging strategies, with marked spatial segregation, but limited evidence of interspecific dietary partitioning. The larger-bodied brown booby foraged within neritic waters, with the smaller-bodied red-footed booby travelling further offshore. Almost no sex differences were detected in foraging behaviour of red-footed boobies, while male and female brown boobies differed in their habitat use, foraging characteristics and dietary contributions. We suggest that these behavioural differences may relate to size dimorphism and competition: In the small brown booby population (n < 200 individuals), larger females showed a higher propensity to remain in coastal waters where they experienced kleptoparasitic attacks from magnificent frigatebirds, while smaller males that were never kleptoparasitised travelled further offshore, presumably into habitats with lower kleptoparasitic pressure. In weakly dimorphic red-footed boobies, these differences are less pronounced. Instead, density-dependent pressures on their large population (n > 2000 individuals) and avoidance of kleptoparasitism may be more prevalent in driving movements for both sexes.ConclusionsOur results reveal how, in an environment where opportunities for prey diversification are limited, neighbouring seabird species segregate at-sea, while exhibiting differing degrees of sexual differentiation. While the mechanisms underlying observed patterns remain unclear, our data are consistent with the idea that multiple factors involving both conspecifics and heterospecifics, as well as reproductive pressures, may combine to influence foraging differences in these neighbouring tropical species.

Caterpillars of the marsh fritillary butterfly Euphydryas aurinia can extend their life-cycle in Scotland

The marsh fritillary Euphydryas aurinia is declining across Europe and is of high conservation interest. Its ecology has been defined and its conservation status assessed primarily from the affinities and populations of young caterpillars in the autumn, before hibernation and high winter mortality. The possibility that caterpillars of E. aurinia can overwinter more than once was investigated on the Isle of Islay, Scotland after caterpillars were found to occur at some locations in the spring despite a pre-hibernation absence. Closely-related species in North America and Northern Europe can prolong larval development by diapausing for a year as does E. aurinia in Scandinavia. Measurements of development and manipulations of distribution confirmed that some caterpillars do extend the life-cycle in Scotland and may occur in areas devoid of larvae in their first year. Caterpillars attempting this life-cycle develop slowly in spring, attain the normal penultimate spring instar and then enter diapause while other caterpillars are pupating. They moult just before diapause, construct highly cryptic webs and on emergence the following spring are 5–6 times heavier than larvae emerging in their first spring, or the equivalent of a month or so ahead. They attain a final, extra instar as larvae in their first spring reach the penultimate instar. Knowledge of this life-cycle is confined in the UK to Islay but its occurrence in this mild climate implies that it is more widespread.Implications for insect conservation Conditions that permit long diapause are probably precise and may not be reflected in recognised qualities of habitat. The species may also be present despite a perceived absence in autumn, the standard period for monitoring. Assessments of the prevalence of the life-cycle and its contribution to the persistence of E. aurinia are required. Populations of E. aurinia are known to fluctuate greatly and do occur below the observation threshold for long periods.

VARIABILITY OF SHELL IN GASTROPODS OF THE GENUS BORYSTHENIA LINDHOLM, 1914: TESTING THE STATISTICAL APPROACH IN SEARCH OF TRAITS FOR THE RECENT AND FOSSIL SPECIES DELIMITATION

The gastropod mollusc genus Borysthenia Lindholm, 1914 comprises many species throughout Europe, Asia, North Africa and North America but species delimitation, based mainly on shell morphology (only possible concerning the fossil records) is often disputable. Statistical methods used to test if the shell measurements are reliable traits in delimitation of recent and fossil species in gastropod molluscs of the genus Borysthenia. Our analyses based on quantitative study of over 100 specimens of the Borysthenia species both modern and fossil. It is concluded that the dimensional characteristics of their shell are suitable for the differentiation of both recent and fossil (at least of Pontian age) species through the statistical processing of quantitative data. Through the morphological study of type material, taxonomic status of B. jalpuchense Gozhik, 2002 and B. vinogradovkaense Gozhik, 2002 described from the middle-pontian deposits of Ukraine revised. It is suggested that these taxa are considered two distinct though close relative extinct species. Stratigraphic range of B. jalpuchense is expanded up to the Lower Pontian. All the modern individuals of Borysthenia involved are attributed to B. menkeana (Jelski, 1863) due to their exact correspondence to the lectotype of this species.

Authentication of medicinal herb Wikstroemia indica using novel DNA markers derived from the chloroplast genome sequences

The processed root of Wikstroemia indica, also known as Wikstroemiae Radix (WR), is known as a time-honored traditional herbal medicine demonstrating health-promoting properties. Although W. indica is valuable, its molecular information on this medicinal plant is limited. In this study, we reported the complete chloroplast (cp) genome sequences of W. indica and its congener, W. nutans, the latter of which is highly identical to W. indica in both their natural distributions and morphological characteristics. The cp genomes of W. indica and W. nutans were 151,746 bp and 149,776 bp in size, respectively, and were predicted to contain the same number of genes, including 78 protein-coding, 37 tRNA, and eight rRNA genes. Genome comparison of W. indica showed that mutational hotspots were present despite low intraspecific variations were detected between two different accessions. Although phylogenetic analyses revealed that the two closely-related species of Wikstroemia were sisters, presence of variations in the sequence and mutational hotspots demarcated these two species apart. To authenticate commercial WR products sold in the market, three sets of novel indel markers and two sets of novel DNA barcoding markers from the cp genome sequences were developed. However, only the indel marker ndhK-trnV and the DNA barcoding marker, ccsA-psaC were proven useful in discriminating W. indica from W. nutans; while the former is even capable to delimit W. indica from adulterants of other related species. The findings of this study are useful for the molecular development of W. indica and also contribute to the effort in species authentication, trade monitoring and drug regulation in the local herbal industry.

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii

Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii’s success and its ongoing adaptation to the human host.

Evolution of immunogenetic components used to form ultralong VH CDR3 antibodies in Bovidae

Abstract Cattle has a restricted repository of immunoglobulin heavy chain gene segments with only one family of V, 4 J and 16 D segments functional. Among these segments are a V and D that, together, encode a heavy chain with an ultralong CDR3 region which manifests as a “stalk” supporting a “knob” domain of which only the knob has antigen binding capability. This antibody structure has boundless therapeutic potential, including for treatment of HIV and other antigens with veiled epitopes. Upon the discovery of this ultralong antibody in Bos taurus, speculation of its origin began. The components that should facilitate ultralong CDR3H antibodies appear in more species than just Bos taurus; they expand throughout the bovine subfamily as evidence by the presence of a V motif “TTVHQ” crested by an 8 base-pair (bp) duplication, and a comparatively long D segment. Several closely-related species encode the ultralong V segments gene in their germline IgH locus. Phylogenetically bookending the cluster that is genomically equipped for the ultralong cattlebody are the species Bos taurus and Bison bison with Bos mutus, indicus, and grunniens in between. The added length of the D segment is less consistent throughout the group as none of the species encode as long of segment as Bos taurus at 50 amino acids. Two species studied, Bos mutus and Bos grunniens, have 15 and 22 amino acids, respectively, encoded by their longest D segment, and Bison bison has 23. Though we do know the germline encodes the ultralong antibody, it is imperative to know if the gene rearrangement is actually expressed and employed in the mature repertoire.

Sex-dependent divergence in asymmetrical reproductive tract morphology between two closely-related amphisbaenian species (Squamata: Amphisbaenidae)

Abstract Comparing reproductive tract morphology between closely-related species may reveal mechanisms and processes leading to reproductive isolation and cladogenesis. Differences in external morphology are often inconspicuous between closely-related Neotropical species, and tissue samples for DNA sequencing are usually scarce for fossorial organisms such as amphisbaenians. Therefore, comparing characters of the reproductive tract between closely related amphisbaenians may be a viable alternative to understand processes by which evolutionary lineages have diverged morphologically from common ancestors. In this study we used multivariate ordination to compare reproductive tract morphology between two closely-related Amphisbaenidae species (Amphisbaena anaemariae and A. silvestrii), which are morphologically similar, and phylogenetically closely related. We tested the hypothesis that interspecific divergence in the reproductive tract may explain mechanisms and processes of reproductive divergence leading to evolutionary divergence. Our results suggest that divergence between two closely related Amphisbaenidae species may be linked with reproductive isolation caused by morphological differences in the reproductive tract. However, the levels of divergence detected varied between sexes and sides of the body on which the variables were measured, with vas deferens length, testis length and diameter and gonad-cloaca length as the determining variables differencing species. Although our findings must be validated by DNA-based analysis, this study provides insights into evolutionary processes based on reproductive divergence mechanisms in organisms for which sampling is hindered by fossoriality.

Interspecies Genomic Variation and Transcriptional Activeness of Secondary Metabolism-Related Genes in Aspergillus Section Fumigati.

Filamentous fungi produce various bioactive compounds that are biosynthesized by sets of proteins encoded in biosynthesis gene clusters (BGCs). For an unknown reason, many BGCs are transcriptionally silent in laboratory conditions, which has hampered the discovery of novel fungal compounds. The transcriptional reactiveness of fungal secondary metabolism is not fully understood. To gain the comprehensive view, we conducted comparative genomic and transcriptomic analyses of nine closely-related species of Aspergillus section Fumigati (A. fumigatus, A. fumigatiaffinis, A. novofumigatus, A. thermomutatus, A. viridinutans, A. pseudoviridinutans, A. lentulus, A. udagawae, and Neosartorya fischeri). For expanding our knowledge, we newly sequenced genomes of A. viridinutans and A. pseudoviridinutans, and reassembled and reannotated the previously released genomes of A. lentulus and A. udagawae. Between 34 and 84 secondary metabolite (SM) backbone genes were identified in the genomes of these nine respective species, with 8.7-51.2% being unique to the species. A total of 247 SM backbone gene types were identified in the nine fungi. Ten BGCs are shared by all nine species. Transcriptomic analysis using A. fumigatus, A. lentulus, A. udagawae, A. viridinutans, and N. fischeri was conducted to compare expression levels of all SM backbone genes in four different culture conditions; 32-83% of SM backbone genes in these species were not expressed in the tested conditions, which reconfirmed that large part of fungal SM genes are hard to be expressed. The species-unique SM genes of the five species were expressed with lower frequency (18.8% in total) than the SM genes that are conserved in all five species (56%). These results suggest that the expression tendency of BGCs is correlated with their interspecies distribution pattern. Our findings increase understanding of the evolutionary processes associated with the regulation of fungal secondary metabolism.

Parataxonomy, perceived dynamics and diversity of uses of two Detarium species in Benin (West Africa)

The contribution of species providing non-timber forest products to the livelihoods of local communities is well established. However, this contribution may be limited by the existence of confusion while dealing with close relative species. This is particularly the case for Detarium microcarpum Guill & Perr. and D. senegalense J.F.Gmel. The objectives of this study were to (1) identify the criteria used by local communities to differentiate D. microcarpum and D. senegalense, (2) determine local communities’ perception of the past dynamics of the two species and (3) assess the diversity of uses of both species. Data on differentiation criteria, perceived variation in the species abundance, and the different uses were collected using individual semi-structured interviews (n = 914 informants). The relative frequency of citation and the use-value were calculated. The Chi-square test, correspondence analysis and generalized linear model were used for statistical analyses. Informants used fourteen criteria to differentiate the two species. The predominant criteria were the shape of the seed (87.86%) and the shape of the fruit (67.86%). Most of the informants reported that the populations of D. microcarpum (61.80%) and that of D. senegalense (60.12%) have regressed. In total, 168 use-reports were enumerated for the two species with 19 shared use-reports. We concluded that local communities use a variety of criteria to differentiate both species, the most popular being morphological traits of the fruits. Both species shared several use-reports (11.31%). However, their populations have declined. The documented uses for both species provide preliminary information for their future food uses and drug discovery.

Vitellogenin gene expression in marine mussels exposed to ethinylestradiol: No induction at the transcriptional level

Vitellogenin (Vtg), a large multidomain protein precursor of egg-yolk proteins, is used as an endocrine disruption biomarker in fish, and in the last decades, its use has been extended to invertebrates like mollusks. However, it remains unclear whether invertebrate endocrine system produces Vtg in response to estrogens, like it occurs in oviparous vertebrates. In a previous study, no evidence of induction of Vtg expression at protein level was found in gonads of the marine mussel Mytilus galloprovincialis after exposure to the estrogenic chemical 17α-ethinylestradiol (EE2). In the present follow-up study, it was investigated whether there is any effect of EE2 on Vtg abundance at transcriptional level in M. galloprovincialis gonads. To this aim, RT-qPCR analysis targeting three different domains of Vtg transcript was performed on gonads of mussels that were exposed either 4 or 24 days to 100 ng/L EE2. In addition, several reference genes were analysed and a selection of these for potential use in further RT-qPCR analyses on mussel male and female gonads is provided. Results showed higher expression in females than in males for the three analysed Vtg domains, and no evidence of Vtg mRNA induction due to EE2 either in females or males. The present results, together with those obtained from previous analysis at protein level, support that Vtg is not an adequate biomarker for xenoestrogenicity in marine mussels. Additionally, nucleotide sequences of Vtg transcripts of three closely-related species from Mytilus edulis complex (M. galloprovincialis, M. edulis and M. trossulus) are provided and compared with Vtg sequences from other mollusk species to assess the level of conservation and evolutionary relationships among species.

Isolation and Molecular Identification of some Fungi Associated with Jatropha curcas (L.)

Jatropha curcas is a plant of great economic importance that experiences high incidence of fungal attack. Misidentification of the fungal species is bound to occur with the use of traditional cultural methods where organisms are identified morphologically and/or microscopically. This study was carried out to isolate and identify the fungi associated with Jatropha curcas (L.) using both traditional/ cultural techniques and molecular methods. The fungi were isolated from diseased leaves and stems of J. curcas using both Standard Blotter and Potato Dextrose Agar (PDA) methods. DNA was extracted from the fungal isolates using Zymo Fungal/Bacteria DNA MiniPrep Kit. Amplification of the Internal Transcribed Spacer (ITS) regions of the fungal isolates was carried out using fungi universal primer pairs for ITS4 and ITS5. The amplicons were sequenced and the isolates were identified as Penicillium brevicompactum, Aspergillus sp., Botryosphaeria rhodina, Aspergillus nomius, Aspergillus tamarii, Rhizopus oryzae, Penicillium citrinum and Fusarium solani. Phylogenetic analysis was carried out to know the relationship between the isolates and other closely-related species in GenBank. Jatropha curcas is colonized by many fungal species some of which may be pathogenic to the plant, and molecular techniques pose the best alternative for accurate identification of these organisms.&#x0D; Keywords: Jatropha curcas, fungi, polymerase chain reaction, phylogeny, sequencing

Antennal transcriptome analysis of olfactory genes and characterizations of odorant binding proteins in two woodwasps, Sirex noctilio and Sirex nitobei (Hymenoptera: Siricidae)

BackgroundThe woodwasp Sirex noctilio Fabricius is a major quarantine pest worldwide that was first discovered in China in 2013 and mainly harms Pinus sylvestris var. mongolica Litv.. S. nitobei Matsumura is a native species in China and is closely related to S. noctilio. Recently, the two woodwasps species were found attacking the P. sylvestris var. mongolica Litv in succession. The olfactory system is the foundation of insect behavior. Olfactory genes were identified through antennal transcriptome analysis. The expression profiles odorant binding proteins (OBPs) were analyzed with RT-qPCR.ResultsFrom our transcriptome analysis, 16 OBPs, 7 chemosensory proteins (CSPs), 41 odorant receptors (ORs), 8 gustatory receptors (GRs), 13 ionotropic receptors (IRs), and one sensory neuron membrane protein (SNMP) were identified in S. noctilio, while 15 OBPs, 6 CSPs, 43 ORs, 10 GRs, 16 IRs, and 1 SNMP were identified in S. nitobei. Most of the olfactory genes identified in two species were homologous. However, some species-specific olfactory genes were identified from the antennal transcriptomes, including SnocOBP13, SnocCSP6, SnocOR26, SnocGR2, SnocIR7 in S. noctilio and SnitGR9, SnitGR11, SnitIR17 in S. nitobei. In total, 14 OBPs were expressed primarily in the antennae. SnocOBP9 and SnitOBP9, identified as PBP homologues, were sex-biased expression in two siricid, but with different pattern. SnocOBP11 and SnitOBP11 were highly expressed in antennae and clearly expressed in external genitalia. SnocOBP7 and SnitOBP7 were highly expressed in male genitalia. SnocOBP3 and SnocOBP10 were highly expressed in female genitalia and male heads, while SnitOBP3 and SnitOBP10 did not show obvious tissue bias.ConclusionWe analyzed 86 and 91 olfactory genes from S. noctilio and S. nitobei, respectively. Most of the olfactory genes identified were homologous, but also some species-specific olfactory genes were identified, which indicated the similarities and differences of the molecular mechanisms between the two closely-related species. Different expression in the antennae, external genitals or heads, exhibiting an obvious sex bias, suggested their different role in recognizing sex pheromones or plant volatiles. Species-specific expression for several OBPs genes may suggest that they strengthened or lost their original function during species differentiation, resulting in olfactory differences between the two species.

Plasticity in timing of avian breeding in response to spring temperature differs between early and late nesting species

Plasticity for breeding dates may influence population vulnerability to climate change via phenological mismatch between an organism’s life cycle requirements and resource availability in occupied environments. Some life history traits may constrain plasticity, however there have been remarkably few comparisons of how closely-related species, differing in key traits, respond to common phenology gradients. We compared population- and individual-level plasticity in clutch initiation dates (CID) in response to spring temperature among five duck species with early- to late-season nesting life histories. Plasticity was strongest in females of the earliest breeding species (common goldeneye [Bucephala clangula], mallard [Anas platyrhynchos], and gadwall [Mareca strepera]), whereas late-nesting lesser scaup (Aythya affinis) and white-winged scoter (Melanitta fusca deglandi) did not respond. These results contrast with previous work in other bird families that suggested late-breeders are generally more flexible. Nevertheless, late-breeding species exhibited annual variation in mean CID, suggesting response to other environmental factors unrelated to spring temperature. Goldeneye and gadwall females varied in their strength of individual plasticity (‘individual × environment’ interactions) and goldeneye and scoter females showed evidence of interannual repeatability of CID. Fitness consequences of CID plasticity in response to spring phenology, including trophic mechanisms and population consequences, warrant investigation.

Thermal reaction norms of key metabolic enzymes reflect divergent physiological and behavioral adaptations of closely related amphipod species

Lake Baikal is inhabited by more than 300 endemic amphipod species, which are narrowly adapted to certain thermal niches due to the high interspecific competition. In contrast, the surrounding freshwater fauna is commonly represented by species with large-scale distribution and high phenotypic thermal plasticity. Here, we investigated the thermal plasticity of the energy metabolism in two closely-related endemic amphipod species from Lake Baikal (Eulimnogammarus verrucosus; stenothermal and Eulimnogammarus cyaneus; eurythermal) and the ubiquitous Holarctic amphipod Gammarus lacustris (eurythermal) by exposure to a summer warming scenario (6–23.6 °C; 0.8 °C d−1). In concert with routine metabolic rates, activities of key metabolic enzymes increased strongly with temperature up to 15 °C in E. verrucosus, whereupon they leveled off (except for lactate dehydrogenase). In contrast, exponential increases were seen in E. cyaneus and G. lacustris throughout the thermal trial (Q10-values: 1.6–3.7). Cytochrome-c-oxidase, lactate dehydrogenase, and 3-hydroxyacyl-CoA dehydrogenase activities were found to be higher in G. lacustris than in E. cyaneus, especially at the highest experimental temperature (23.6 °C). Decreasing gene expression levels revealed some thermal compensation in E. cyaneus but not in G. lacustris. In all species, shifts in enzyme activities favored glycolytic energy generation in the warmth. The congruent temperature-dependencies of enzyme activities and routine metabolism in E. verrucosus indicate a strong feedback-regulation of enzymatic activities by whole organism responses. The species-specific thermal reaction norms reflect the different ecological niches, including the spatial distribution, distinct thermal behavior such as temperature-dependent migration, movement activity, and mating season.

Evaluation of Autof MS 1000 and Vitek MS MALDI-TOF MS System in Identification of Closely-Related Yeasts Causing Invasive Fungal Diseases.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been accepted as a rapid, accurate, and less labor-intensive method in the identification of microorganisms in clinical laboratories. However, there is limited data on systematic evaluation of its effectiveness in the identification of phylogenetically closely-related yeast species. In this study, we evaluated two commercially available MALDI-TOF systems, Autof MS 1000 and Vitek MS, for the identification of yeasts within closely-related species complexes. A total of 1,228 yeast isolates, representing 14 different species of five species complexes, including 479 of Candida parapsilosis complex, 323 of Candida albicans complex, 95 of Candida glabrata complex, 16 of Candida haemulonii complex (including two Candida auris), and 315 of Cryptococcus neoformans complex, collected under the National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) program, were studied. Autof MS 1000 and Vitek MS systems correctly identified 99.2% and 89.2% of the isolates, with major error rate of 0.4% versus 1.6%, and minor error rate of 0.1% versus 3.5%, respectively. The proportion of isolates accurately identified by Autof MS 1000 and Vitek MS per each yeast complex, respectively, was as follows; C. albicans complex, 99.4% vs 96.3%; C. parapsilosis complex, 99.0% vs 79.1%; C glabrata complex, 98.9% vs 94.7%; C. haemulonii complex, 100% vs 93.8%; and C. neoformans, 99.4% vs 95.2%. Overall, Autof MS 1000 exhibited good capacity in yeast identification while Vitek MS had lower identification accuracy, especially in the identification of less common species within phylogenetically closely-related species complexes.

Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum.

The American cranberry (Vaccinium macrocarpon Ait.) is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genome assembly. Here, we report the first chromosome-scale genome assembly of cranberry, cultivar Stevens, and a draft genome of its close wild relative species Vaccinium microcarpum. More than 92% of the estimated cranberry genome size (492 Mb) was assembled into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative genomics. Our analysis revealed two polyploidization events, the ancient γ-triplication, and a more recent whole genome duplication shared with other members of the Ericaeae, Theaceae and Actinidiaceae families approximately 61 Mya. Furthermore, comparative genomics within the Vaccinium genus suggested cranberry-V. microcarpum divergence occurred 4.5 Mya, following their divergence from blueberry 10.4 Mya, which agrees with morphological differences between these species and previously identified duplication events. Finally, we identified a cluster of subgroup-6 R2R3 MYB transcription factors within a genomic region spanning a large QTL for anthocyanin variation in cranberry fruit. Phylogenetic analysis suggested these genes likely act as anthocyanin biosynthesis regulators in cranberry. Undoubtedly, these new cranberry genomic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level.