Species boundaries in plant pathogenic fungi: a Colletotrichum case study

BACKGROUND

Accurate delimitation of plant pathogenic fungi is critical for the establishment of quarantine regulations, screening for genetic resistance to plant pathogens, and the study of ecosystem function. Concatenation analysis of multi-locus DNA sequence data represents a powerful and commonly used approach to recognizing evolutionary independent lineages in fungi. It is however possible to mask the discordance between individual gene trees, thus the speciation events might be erroneously estimated if one simply recognizes well supported clades as distinct species without implementing a careful examination of species boundary. To investigate this phenomenon, we studied Colletotrichum siamense s. lat., which is a cosmopolitan pathogen causing serious diseases on many economically important plant hosts. Presently there are significant disagreements among mycologists as to what constitutes a species in C. siamense s. lat., with the number of accepted species ranging from one to seven.

RESULTS

In this study, multiple approaches were used to test the null hypothesis "C. siamense is a species complex", using a global strain collection. Results of molecular analyses based on the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and coalescent methods (e.g. Generalized Mixed Yule-coalescent and Poisson Tree Processes) do not support the recognition of any independent evolutionary lineages within C. siamense s. lat. as distinct species, thus rejecting the null hypothesis. This conclusion is reinforced by the recognition of genetic recombination, cross fertility, and the comparison of ecological and morphological characters. Our results indicate that reproductive isolation, geographic and host plant barriers to gene flow are absent in C. siamense s. lat.

CONCLUSIONS

This discovery emphasized the importance of a polyphasic approach when describing novel species in morphologically conserved genera of plant pathogenic fungi.

Patterns of Genetic Variability in Island Populations of the Cane Toad (Rhinella marina) from the Mouth of the Amazon

The Amazonian coast has several unique geological characteristics resulting from the interaction between drainage pattern of the Amazon River and the Atlantic Ocean. It is one of the most extensive and sedimentologically dynamic regions of the world, with a large number of continental islands mostly formed less than 10,000 years ago. The natural distribution of the cane toad (Rhinella marina), one of the world's most successful invasive species, in this complex Amazonian system provides an intriguing model for the investigation of the effects of isolation or the combined effects of isolation and habitat dynamic changes on patterns of genetic variability and population differentiation. We used nine fast-evolving microsatellite loci to contrast patterns of genetic variability in six coastal (three mainlands and three islands) populations of the cane toad near the mouth of the Amazon River. Results from Bayesian multilocus clustering approach and Discriminant Analyses of Principal Component were congruent in showing that each island population was genetically differentiated from the mainland populations. All FST values obtained from all pairwise comparisons were significant, ranging from 0.048 to 0.186. Estimates of both recent and historical gene flow were not significantly different from zero across all population pairs, except the two mainland populations inhabiting continuous habitats. Patterns of population differentiation, with a high level of population substructure and absence/restricted gene flow, suggested that island populations of R. marina are likely isolated since the Holocene sea-level rise. However, considering the similar levels of genetic variability found in both island and mainland populations, it is reliable to assume that they were also isolated for longer periods. Given the genetic uniqueness of each cane toad population, together with the high natural vulnerability of the coastal regions and intense human pressures, we suggest that these populations should be treated as discrete units for conservation management purposes.

Biocomplexity in Populations of European Anchovy in the Adriatic Sea

The sustained exploitation of marine populations requires an understanding of a species' adaptive seascape so that populations can track environmental changes from short- and long-term climate cycles and from human development. The analysis of the distributions of genetic markers among populations, together with correlates of life-history and environmental variability, can provide insights into the extent of adaptive variation. Here, we examined genetic variability among populations of mature European anchovies (n = 531) in the Adriatic (13 samples) and Tyrrhenian seas (2 samples) with neutral and putative non-neutral microsatellite loci. These genetic markers failed to confirm the occurrence of two anchovy species in the Adriatic Sea, as previously postulated. However, we found fine-scale population structure in the Adriatic, especially in northern areas, that was associated with four of the 13 environmental variables tested. Geographic gradients in sea temperature, salinity and dissolved oxygen appear to drive adaptive differences in spawning time and early larval development among populations. Resolving adaptive seascapes in Adriatic anchovies provides a means to understand mechanisms underpinning local adaptation and a basis for optimizing exploitation strategies for sustainable harvests.

The origin of Chinese domestic horses revealed with novel mtDNA variants

The origin of domestic horses in China was a controversial issue and several hypotheses including autochthonous domestication, introduction from other areas, and multiple-origins from both introduction and local wild horse introgression have been proposed, but none of them have been fully supported by DNA data. In the present study, mitochondrial DNA (mtDNA) sequences of 714 Chinese indigenous horses were analyzed. The results showed that Chinese domestic horses harbor some novel mtDNA haplogroups and suggested that local domestication events may have occurred, but they are not the dominant haplogroups and the geographical distributions of the novel mtDNA haplogroups were rather restricted. Conclusively, our results support the hypothesis that the domestic horses in China originated from both the introduced horses from outside of China and the local wild horses' introgression into the domestic populations. Results of genetic diversity analysis suggested a possibility that the introduced horses entered China through northern regions from the Eurasian steppe.

Genomic variation among populations of threatened coral: Acropora cervicornis

Background

Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species’ ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef Tract (FRT) and in the Dominican Republic.

Results

Genotyping by Sequencing (GBS) identified 4,764 single nucleotide polymorphisms (SNPs). Pairwise nucleotide differences (π) within a population are large (~37 %) and similar to π across all individuals. This high level of genetic diversity along the FRT is similar to the diversity within a small, isolated reef. Much of the genetic diversity (>90 %) exists within a population, yet GBS analysis shows significant variation along the FRT, including 300 SNPs with significant F_ST values and significant divergence relative to distance. There are also significant differences in SNP allele frequencies over small spatial scales, exemplified by the large F_ST values among corals collected within Miami-Dade county.

Conclusions

Large standing diversity was found within each population even after recent declines in abundance, including significant, potentially adaptive divergence over short distances. The data here inform conservation and management actions by uncovering population structure and high levels of diversity maintained within coral collections among sites previously shown to have little genetic divergence. More broadly, this approach demonstrates the power of GBS to resolve differences among individuals and identify subtle genetic structure, informing conservation goals with evolutionary implications.

Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species

Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches which presently harbor these populations operate as refugia during the current interglacial. However, owing to limitations of the standard phylogeographic approaches used in these studies, this hypothesis was not explicitly tested. Here we use Approximate Bayesian Computation to refine the previous inferences and test the role of different events in the diversification of two species within P. aurisetus group. We used molecular data from chloroplast DNA and simple sequence repeats loci of P. machrisii and P. aurisetus, the two species with broadest distribution in the complex, in order to test if the diversification in each species was driven mostly by vicariance or by long-dispersal events. We found that both species were affected primarily by vicariance, with a refuge model as the most likely scenario for P. aurisetus and a soft vicariance scenario most probable for P. machrisii. These results emphasize the importance of distributional fragmentation in these species, and add support to the hypothesis of long-term isolation in interglacial refugia previously proposed for the P. aurisetus species complex diversification.

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels

Vertebrate gut microbiome often underpins the metabolic capability and provides many beneficial effects on their hosts. However, little was known about how host trophic level influences fish gut microbiota and metabolic activity. In this study, more than 985,000 quality-filtered sequences from 24 16S rRNA libraries were obtained and the results revealed distinct compositions and diversities of gut microbiota in four trophic categories. PCoA test showed that gut bacterial communities of carnivorous and herbivorous fishes formed distinctly different clusters in PCoA space. Although fish in different trophic levels shared a large size of OTUs comprising a core microbiota community, at the genus level a strong distinction existed. Cellulose-degrading bacteria Clostridium, Citrobacter and Leptotrichia were dominant in the herbivorous, while Cetobacterium and protease-producing bacteria Halomonas were dominant in the carnivorous. PICRUSt predictions of metagenome function revealed that fishes in different trophic levels affected the metabolic capacity of their gut microbiota. Moreover, cellulase and amylase activities in herbivorous fishes were significantly higher than in the carnivorous, while trypsin activity in the carnivorous was much higher than in the herbivorous. These results indicated that host trophic level influenced the structure and composition of gut microbiota, metabolic capacity and gut content enzyme activity.

Detection ofBartonellaspp. in wild carnivores, hyraxes, hedgehog and rodents from Israel

Bartonellainfection was explored in wild animals from Israel. Golden jackals (Canis aureus), red foxes (Vulpes vulpes), rock hyraxes (Procavia capensis), southern white-breasted hedgehogs (Erinaceus concolor), social voles (Microtus socialis), Tristram's jirds (Meriones tristrami), Cairo spiny mice (Acomys cahirinus), house mice (Mus musculus) and Indian crested porcupines (Hystrix indica) were sampled and screened by molecular and isolation methods.Bartonella-DNA was detected in 46 animals: 9/70 (13%) golden jackals, 2/11 (18%) red foxes, 3/35 (9%) rock hyraxes, 1/3 (33%) southern white-breasted hedgehogs, 5/57 (9%) Cairo spiny mice, 25/43 (58%) Tristram's jirds and 1/6 (16%) house mice.Bartonella rochalimaeandB. rochalimae-like were widespread among jackals, foxes, hyraxes and jirds. This report represents the first detection of this zoonoticBartonellasp. in rock hyraxes and golden jackals. Moreover, DNA ofBartonella vinsoniisubsp.berkhoffii, Bartonella acomydis, CandidatusBartonella merieuxii and other uncharacterized genotypes were identified. Three differentBartonellastrains were isolated from Tristram's jirds, and several genotypes were molecularly detected from these animals. Furthermore, this study reports the first detection ofBartonellainfection in a southern hedgehog. Our study indicates that infection with zoonotic and otherBartonellaspecies is widespread among wild animals and stresses their potential threat to public health.

The genetic contribution to sex determination and number of sex chromosomes vary among populations of common frogs (Rana temporaria)

The patterns of sex determination and sex differentiation have been shown to differ among geographic populations of common frogs. Notably, the association between phenotypic sex and linkage group 2 (LG2) has been found to be perfect in a northern Swedish population, but weak and variable among families in a southern one. By analyzing these populations with markers from other linkage groups, we bring two new insights: (1) the variance in phenotypic sex not accounted for by LG2 in the southern population could not be assigned to genetic factors on other linkage groups, suggesting an epigenetic component to sex determination; (2) a second linkage group (LG7) was found to co-segregate with sex and LG2 in the northern population. Given the very short timeframe since post-glacial colonization (in the order of 1000 generations) and its seemingly localized distribution, this neo-sex chromosome system might be the youngest one described so far. It does not result from a fusion, but more likely from a reciprocal translocation between the original Y chromosome (LG2) and an autosome (LG7), causing their co-segregation during male meiosis. By generating a strict linkage between several important genes from the sex-determination cascade (Dmrt1, Amh and Amhr2), this neo-sex chromosome possibly contributes to the 'differentiated sex race' syndrome (strictly genetic sex determination and early gonadal development) that characterizes this northern population.

Characterization of functional trait diversity among Indian cultivated and weedy rice populations

Weedy rice, a menace in rice growing areas globally, is biosimilar having attributes similar to cultivated and wild rice, and therefore is difficult to manage. A study was initiated to characterize the functional traits of 76 weedy rice populations and commonly grown rice cultivars from different agro-climatic zones for nine morphological, five physiological, and three phenological parameters in a field experiment under an augmented block design. Comparison between weedy and cultivated rice revealed a difference in duration (days) from panicle emergence to heading as the most variable trait and awn length as the least variable one, as evidenced from their coefficients of variation. The results of principal component analysis revealed the first three principal components to represent 47.3% of the total variation, which indicates an important role of transpiration, conductance, leaf-air temperature difference, days to panicle emergence, days to heading, flag leaf length, SPAD (soil-plant analysis development), grain weight, plant height, and panicle length to the diversity in weedy rice populations. The variations existing in weedy rice population are a major reason for its wider adaptability to varied environmental conditions and also a problem while trying to manage it.

Molecular Phylogeny and Biogeography of the Amphidromous Fish Genus Dormitator Gill 1861 (Teleostei: Eleotridae)

Species of the genus Dormitator, also known as sleepers, are representatives of the amphidromous freshwater fish fauna that inhabit the tropical and subtropical coastal environments of the Americas and Western Africa. Because of the distribution of this genus, it could be hypothesized that the evolutionary patterns in this genus, including a pair of geminate species across the Central American Isthmus, could be explained by vicariance following the break-up of Gondwana. However, the evolutionary history of this group has not been evaluated. We constructed a time-scaled molecular phylogeny of Dormitator using mitochondrial (Cytochrome b) and nuclear (Rhodopsin and β-actin) DNA sequence data to infer and date the cladogenetic events that drove the diversification of the genus and to relate them to the biogeographical history of Central America. Two divergent lineages of Dormitator were recovered: one that included all of the Pacific samples and another that included all of the eastern and western Atlantic samples. In contrast to the Pacific lineage, which showed no phylogeographic structure, the Atlantic lineage was geographically structured into four clades: Cameroon, Gulf of Mexico, West Cuba and Caribbean, showing evidence of potential cryptic species. The separation of the Pacific and Atlantic lineages was estimated to have occurred ~1 million years ago (Mya), whereas the four Atlantic clades showed mean times of divergence between 0.2 and 0.4 Mya. The splitting times of Dormitator between ocean basins are similar to those estimated for other geminate species pairs with shoreline estuarine preferences, which may indicate that the common evolutionary histories of the different clades are the result of isolation events associated with the closure of the Central American Isthmus and the subsequent climatic and oceanographic changes.

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome‐wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late‐season drought in California. These ancestor‐descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (F_ST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome‐wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution.

see also the Perspective by Hancock

Maintenance of a Protein Structure in the Dynamic Evolution of TIMPs over 600 Million Years

Deciphering the events leading to protein evolution represents a challenge, especially for protein families showing complex evolutionary history. Among them, TIMPs represent an ancient eukaryotic protein family widely distributed in the animal kingdom. They are known to control the turnover of the extracellular matrix and are considered to arise early during metazoan evolution, arguably tuning essential features of tissue and epithelial organization. To probe the structure and molecular evolution of TIMPs within metazoans, we report the mining and structural characterization of a large data set of TIMPs over approximately 600 Myr. The TIMPs repertoire was explored starting from the Cnidaria phylum, coeval with the origins of connective tissue, to great apes and humans. Despite dramatic sequence differences compared with highest metazoans, the ancestral proteins displayed the canonical TIMP fold. Only small structural changes, represented by an α-helix located in the N-domain, have occurred over the evolution. Both the occurrence of such secondary structure elements and the relative solvent accessibility of the corresponding residues in the three-dimensional structures raises the possibility that these sites represent unconserved element prone to accept variations.

Testing the island effect on phenotypic diversification: insights from the Hemidactylus geckos of the Socotra Archipelago

Island colonization is often assumed to trigger extreme levels of phenotypic diversification. Yet, empirical evidence suggests that it does not always so. In this study we test this hypothesis using a completely sampled mainland-island system, the arid clade of Hemidactylus, a group of geckos mainly distributed across Africa, Arabia and the Socotra Archipelago. To such purpose, we generated a new molecular phylogeny of the group on which we mapped body size and head proportions. We then explored whether island and continental taxa shared the same morphospace and differed in their disparities and tempos of evolution. Insular species produced the most extreme sizes of the radiation, involving accelerated rates of evolution and higher disparities compared with most (but not all) of the continental groups. In contrast, head proportions exhibited constant evolutionary rates across the radiation and similar disparities in islands compared with the continent. These results, although generally consistent with the notion that islands promote high morphological disparity, reveal at the same time a complex scenario in which different traits may experience different evolutionary patterns in the same mainland-island system and continental groups do not always present low levels of morphological diversification compared to insular groups.

Fast and sensitive taxonomic classification for metagenomics with Kaiju

Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows–Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk.

Here, Anders Krogh and colleagues describe Kaiju, a metagenome taxonomic classification program that uses maximum (in-)exact matches on the protein-level to account for evolutionary divergence. The authors show that Kaiju performs faster and is more sensitive compared with existing algorithms and can be used on a standard computer.

Interspecific and environment-induced variation in hypoxia tolerance in sunfish

Hypoxia tolerance is a plastic trait, and can vary between species. We compared hypoxia tolerance (hypoxic loss of equilibrium, LOE, and critical O2 tension, Pcrit) and traits that dictate O2 transport and metabolism in pumpkinseed (Lepomis gibbosus), bluegill (L. macrochirus), and the naturally occurring hybrid in different acclimation environments (wild versus lab-acclimated fish) and at different temperatures. Wild fish generally had lower Pcrit and lower PO2 at LOE in progressive hypoxia than lab-acclimated fish, but time to LOE in sustained hypoxia (PO2 of 2kPa) did not vary between environments. Wild fish also had greater gill surface area and higher haematocrit, suggesting that increased O2 transport capacity underlies the environmental variation in Pcrit. Metabolic (lactate dehydrogenase, LDH; pyruvate kinase, PK; citrate synthase; cytochrome c oxidase) and antioxidant (catalase and superoxide dismutase) enzyme activities varied appreciably between environments. Wild fish had higher protein contents across tissues and higher activities of LDH in heart, PK in brain, and catalase in brain, liver, and skeletal muscle. Otherwise, wild fish had lower activities for most enzymes. Warming temperature from 15 to 25°C increased O2 consumption rate, Pcrit, PO2 at LOE, and haemoglobin-O2 affinity, and decreased time to LOE, but pumpkinseed had ≥2-fold longer time to LOE than bluegill and hybrids across this temperature range. This was associated with higher LDH activities in the heart and muscle, and lower or similar antioxidant enzyme activities in several tissues. However, the greater hypoxia tolerance of pumpkinseed collapsed at 28°C, demonstrating that the interactive effects of hypoxia and warming temperature can differ between species. Overall, distinct mechanisms appear to underpin interspecific and environment-induced variation in hypoxia tolerance in sunfish.

Factors influencing the effect size distribution of adaptive substitutions

The distribution of effect sizes of adaptive substitutions has been central to evolutionary biology since the modern synthesis. Early theory proposed that because large-effect mutations have negative pleiotropic consequences, only small-effect mutations contribute to adaptation. More recent theory suggested instead that large-effect mutations could be favoured when populations are far from their adaptive peak. Here we suggest that the distributions of effect sizes are expected to differ among study systems, reflecting the wide variation in evolutionary forces and ecological conditions experienced in nature. These include selection, mutation, genetic drift, gene flow, and other factors such as the degree of pleiotropy, the distance to the phenotypic optimum, whether the optimum is stable or moving, and whether new mutation or standing genetic variation provides the source of adaptive alleles. Our goal is to review how these factors might affect the distribution of effect sizes and to identify new research directions. Until more theory and empirical work is available, we feel that it is premature to make broad generalizations about the effect size distribution of adaptive substitutions important in nature.

Reconstruction of phylogenetic relationships in dermatomycete genus Trichophyton Malmsten 1848 based on ribosomal internal transcribed spacer region, partial 28S rRNA and beta-tubulin genes sequences

Trichophyton spp. are important causative agents of superficial mycoses. The phylogeny of the genus and accurate strain identification, based on the ribosomal ITS region sequencing, are still under development. The present work is aimed at (i) inferring the genus phylogeny from partial ITS, LSU and BT2 sequences (ii) description of ribosomal ITS region polymorphism in 15 strains of Trichophyton interdigitale. We performed DNA sequence-based species identification and phylogenetic analysis on 48 strains belonging to the genus Trichophyton. Phylogenetic relationships were inferred by maximum likelihood and Bayesian methods on concatenated ITS, LSU and BT2 sequences. Ribosomal ITS region polymorphisms were assessed directly on the alignment. By phylogenetic reconstruction, we reveal major anthropophilic and zoophilic species clusters in the genus Trichophyton. We describe several sequences of the ITS region of T. interdigitale, which do not fit in the traditional polymorphism scheme and propose emendations in this scheme for discrimination between ITS sequence types in T. interdigitale. The new polymorphism scheme will allow inclusion of a wider spectrum of isolates while retaining its explanatory power. This scheme was also found to be partially congruent with NTS typing technique.

Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts

The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene-space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution.

Highly polymorphic colour vision in a New World monkey with red facial skin, the bald uakari (Cacajao calvus)

Colour vision is highly variable in New World monkeys (NWMs). Evidence for the adaptive basis of colour vision in this group has largely centred on environmental features such as foraging benefits for differently coloured foods or predator detection, whereas selection on colour vision for sociosexual communication is an alternative hypothesis that has received little attention. The colour vision of uakaris (Cacajao) is of particular interest because these monkeys have the most dramatic red facial skin of any primate, as well as a unique fission/fusion social system and a specialist diet of seeds. Here, we investigate colour vision in a wild population of the bald uakari,C. calvus, by genotyping the X-linked opsin locus. We document the presence of a polymorphic colour vision system with an unprecedented number of functional alleles (six), including a novel allele with a predicted maximum spectral sensitivity of 555 nm. This supports the presence of strong balancing selection on different alleles at this locus. We consider different hypotheses to explain this selection. One possibility is that trichromacy functions in sexual selection, enabling females to choose high-quality males on the basis of red facial coloration. In support of this, there is some evidence that health affects facial coloration in uakaris, as well as a high prevalence of blood-borne parasitism in wild uakari populations. Alternatively, the low proportion of heterozygous female trichromats in the population may indicate selection on different dichromatic phenotypes, which might be related to cryptic food coloration. We have uncovered unexpected diversity in the last major lineage of NWMs to be assayed for colour vision, which will provide an interesting system to dissect adaptation of polymorphic trichromacy.

Divergence and isolation of cryptic sympatric taxa within the annual legume Amphicarpaea bracteata

The amphicarpic annual legume Amphicarpaea bracteata is unusual in producing aerial and subterranean cleistogamous flowers that always self‐fertilize and, less commonly, aerial chasmogamous flowers that outcross. Although both morphologic and genetic variants are known in this highly selfing species, debate continues over whether this variation is continuous, reflecting the segregation of standing genetic variation, or discontinuous, reflecting distinct taxa that rarely intercross. We characterized SNP variation in 128 individuals in southern Wisconsin to assess within‐ and among‐population variation at 3928 SNPs. We also assessed genotype and leaf morphology in an additional 76 individuals to connect phenotypic variation with genetic variation. Genetic variation maps onto three strongly divergent and highly inbred genetic groups showing little relation to site location. Each group has a distinct phenotype, but the divergence of these groups differs from the varietal divisions previously identified based on morphological characters. Like previous authors, we argue that the taxonomy of this species should be revised. Despite extensive sympatry, estimates of among‐group migration rates are low, and hybrid individuals were at low frequency (<2%) in our dataset. Restricted gene flow likely results from high selfing rates and partial reproductive incompatibility as evidenced by the U‐shaped distribution of pairwise F_ST values reflecting “islands” of genomic divergence. These islands may be associated with hybrid incompatibility loci that arose in allopatry. The coexistence of lineages within sites may reflect density‐dependent attack by species‐specific strains of pathogenic fungi and/or root‐nodulating bacteria specializing on distinct genotypes.

Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects

Background

Hybrid breakdown has been well documented in various species. Relationships between genomic heterozygosity and traits-fitness have been extensively explored especially in the natural populations. But correlations between genomic heterozygosity and vegetative and reproductive traits in cotton interspecific populations have not been studied. In the current study, two reciprocal F₂ populations were developed using Gossypium hirsutum cv. Emian 22 and G. barbadense acc. 3–79 as parents to study hybrid breakdown in cotton. A total of 125 simple sequence repeat (SSR) markers were used to genotype the two F₂ interspecific populations.

Results

To guarantee mutual independence among the genotyped markers, the 125 SSR markers were checked by the linkage disequilibrium analysis. To our knowledge, this is a novel approach to evaluate the individual genomic heterozygosity. After marker checking, 83 common loci were used to assess the extent of genomic heterozygosity. Hybrid breakdown was found extensively in the two interspecific F₂ populations particularly on the reproductive traits because of the infertility and the bare seeds. And then, the relationships between the genomic heterozygosity and the vegetative reproductive traits were investigated. The only relationships between hybrid breakdown and heterozygosity were observed in the (Emian22 × 3–79) F₂ population for seed index (SI) and boll number per plant (BN). The maternal cytoplasmic environment may have a significant effect on genomic heterozygosity and on correlations between heterozygosity and reproductive traits.

Conclusions

A novel approach was used to evaluate genomic heterozygosity in cotton; and hybrid breakdown was observed in reproductive traits in cotton. These findings may offer new insight into hybrid breakdown in allotetraploid cotton interspecific hybrids, and may be useful for the development of interspecific hybrids for cotton genetic improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0366-5) contains supplementary material, which is available to authorized users.

DELAY OF GERMINATION1 (DOG1) regulates both seed dormancy and flowering time through microRNA pathways

Seed germination and flowering, two critical developmental transitions in plant life cycles, are coordinately regulated by genetic and environmental factors to match plant establishment and reproduction to seasonal cues. The DELAY OF GERMINATION1 (DOG1) gene is involved in regulating seed dormancy in response to temperature and has also been associated genetically with pleiotropic flowering phenotypes across diverse Arabidopsis thaliana accessions and locations. Here we show that DOG1 can regulate seed dormancy and flowering times in lettuce (Lactuca sativa, Ls) and Arabidopsis through an influence on levels of microRNAs (miRNAs) miR156 and miR172. In lettuce, suppression of LsDOG1 expression enabled seed germination at high temperature and promoted early flowering in association with reduced miR156 and increased miR172 levels. In Arabidopsis, higher miR156 levels resulting from overexpression of the MIR156 gene enhanced seed dormancy and delayed flowering. These phenotypic effects, as well as conversion of MIR156 transcripts to miR156, were compromised in DOG1 loss-of-function mutant plants, especially in seeds. Overexpression of MIR172 reduced seed dormancy and promoted early flowering in Arabidopsis, and the effect on flowering required functional DOG1 Transcript levels of several genes associated with miRNA processing were consistently lower in dry seeds of Arabidopsis and lettuce when DOG1 was mutated or its expression was reduced; in contrast, transcript levels of these genes were elevated in a DOG1 gain-of-function mutant. Our results reveal a previously unknown linkage between two critical developmental phase transitions in the plant life cycle through a DOG1-miR156-miR172 interaction.

Contrasting genetic patterns between two coexisting Eleutherococcus species in northern China

Climate oscillations are the key factors to understand the patterns in modern biodiversity. East Asia harbors the most diverse temperate flora, largely because an extensive terrestrial ice cap was absent during repeated Pleistocene glaciation-interglacial cycles. Comparing the demographic histories of species that are codistributed and are close relatives may provide insight into how the process of climate change influences species ranges. In this study, we compared the spatial genetic structure and demographic histories of two coexisting Eleutherococcus species, Eleutherococcus senticosus and E. sessiliflorus. Both species are distributed in northern China, regions that are generally considered to be sensitive to climatic fluctuations. These regions once hosted temperate forest, but this temperate forest was replaced by tundra and taiga forest during the Last Glacial Maximum (LGM), according to pollen records. Using three chloroplast DNA fragments, we assessed the genetic structure of 20 and 9 natural populations of E. senticosus and E. sessiliflorus, respectively. Extremely contrasting genetic patterns were found between the two species; E. sessiliflorus had little genetic variation, whereas E. senticosus had considerably higher levels of genetic variation (15 haplotypes). We speculated that a recent severe bottleneck may have resulted in the extremely low genetic diversity in E. sessiliflorus. In E. senticosus, populations in Northeast China (NEC) harbored all of the haplotypes found in this species and included private haplotypes. The populations in NEC had higher levels of genetic diversity than did those from North China (NC). Therefore, we suggest that both the NC and NEC regions can sustain LGM refugia and that lineage admixture from multiple refugia took place after the LGM elevated the local genetic diversity in NEC. In NEC, multiple genetic hot spots were found in the Changbai Mountains and the Xiaoxing'an Range, which implied that multiple locations in NEC may sustain LGM refugia, even in the Xiaoxing'an Range.

Assessment of the Genetic Diversity of Different Job's Tears (Coix lacryma-jobi L.) Accessions and the Active Composition and Anticancer Effect of Its Seed Oil

Job's tears (Coix lachryma-jobi L.) is an important crop used as food and herbal medicine in Asian countries. A drug made of Job's tears seed oil has been clinically applied to treat multiple cancers. In this study, the genetic diversity of Job's tears accessions and the fatty acid composition, triglyceride composition, and anti-proliferative effect of Job's tears seed oil were analyzed using morphological characteristics and ISSR markers, GC-MS, HPLC-ELSD, and the MTT method. ISSR analysis demonstrated low genetic diversity of Job's tears at the species level (h = 0.21, I = 0.33) and the accession level (h = 0.07, I = 0.10), and strong genetic differentiation (GST = 0.6702) among all accessions. It also clustered the 11 accessions into three cultivated clades corresponding with geographical locations and two evidently divergent wild clades. The grouping patterns based on morphological characteristics and chemical profiles were in accordance with those clustered by ISSR analysis. Significant differences in morphological characteristics, fatty acid composition, triglyceride composition, and inhibition rates of seed oil were detected among different accessions, which showed a highly significant positive correlation with genetic variation. These results suggest that the seed morphological characteristics, fatty acid composition, and triglyceride composition may be mainly attributed to genetic factors. The proportion of palmitic acid and linoleic acid to oleic acid displayed a highly significant positive correlation with the inhibition rates of Job's tears seed oil for T24 cells, and thus can be an important indicator for quality control for Job's tears.

Evidence of new species for malaria vector Anopheles nuneztovari sensu lato in the Brazilian Amazon region

BACKGROUND

Anopheles nuneztovari sensu lato comprises cryptic species in northern South America, and the Brazilian populations encompass distinct genetic lineages within the Brazilian Amazon region. This study investigated, based on two molecular markers, whether these lineages might actually deserve species status.

METHODS

Specimens were collected in five localities of the Brazilian Amazon, including Manaus, Careiro Castanho and Autazes, in the State of Amazonas; Tucuruí, in the State of Pará; and Abacate da Pedreira, in the State of Amapá, and analysed for the COI gene (Barcode region) and 12 microsatellite loci. Phylogenetic analyses were performed using the maximum likelihood (ML) approach. Intra and inter samples genetic diversity were estimated using population genetics analyses, and the genetic groups were identified by means of the ML, Bayesian and factorial correspondence analyses and the Bayesian analysis of population structure.

RESULTS

The Barcode region dataset (N = 103) generated 27 haplotypes. The haplotype network suggested three lineages. The ML tree retrieved five monophyletic groups. Group I clustered all specimens from Manaus and Careiro Castanho, the majority of Autazes and a few from Abacate da Pedreira. Group II clustered most of the specimens from Abacate da Pedreira and a few from Autazes and Tucuruí. Group III clustered only specimens from Tucuruí (lineage III), strongly supported (97 %). Groups IV and V clustered specimens of A. nuneztovari s.s. and A. dunhami, strongly (98 %) and weakly (70 %) supported, respectively. In the second phylogenetic analysis, the sequences from GenBank, identified as A. goeldii, clustered to groups I and II, but not to group III. Genetic distances (Kimura-2 parameters) among the groups ranged from 1.60 % (between I and II) to 2.32 % (between I and III). Microsatellite data revealed very high intra-population genetic variability. Genetic distances showed the highest and significant values (P = 0.005) between Tucuruí and all the other samples, and between Abacate da Pedreira and all the other samples. Genetic distances, Bayesian (Structure and BAPS) analyses and FCA suggested three distinct biological groups, supporting the barcode region results.

CONCLUSIONS

The two markers revealed three genetic lineages for A. nuneztovari s.l. in the Brazilian Amazon region. Lineages I and II may represent genetically distinct groups or species within A. goeldii. Lineage III may represent a new species, distinct from the A. goeldii group, and may be the most ancestral in the Brazilian Amazon. They may have differences in Plasmodium susceptibility and should therefore be investigated further.

Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera

Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.

Adaptation to Global Change: A Transposable Element-Epigenetics Perspective

Understanding how organisms cope with global change is a major scientific challenge. The molecular pathways underlying rapid adaptive phenotypic responses to global change remain poorly understood. Here, we highlight the relevance of two environment-sensitive molecular elements: transposable elements (TEs) and epigenetic components (ECs). We first outline the sensitivity of these elements to global change stressors and review how they interact with each other. We then propose an integrative molecular engine coupling TEs and ECs and allowing organisms to fine-tune phenotypes in a real-time fashion, adjust the production of phenotypic and genetic variation, and produce heritable phenotypes with different levels of transmission fidelity. We finally discuss the implications of this molecular engine in the context of global change.

An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism

An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus Morbillivirus, currently referred to as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947 bats were investigated originating from 52 capture sites (22 caves, 18 buildings, and 12 outdoor sites) distributed over different bioclimatic zones of the island. Using RT-PCR targeting the L-polymerase gene of the Paramyxoviridae family, we found that 10.5% of sampled bats were infected, representing six out of seven families and 15 out of 31 species analyzed. Univariate analysis indicates that both abiotic and biotic factors may promote viral infection. Using generalized linear modeling of UMRV infection overlaid on biotic and abiotic variables, we demonstrate that sympatric occurrence of bats is a major factor for virus transmission. Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy bats are UMRVs and showed little host specificity. Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that host-switching, rather than co-speciation, is the dominant macro-evolutionary mechanism of UMRVs among Malagasy bats.

Long-term demographic decline and late glacial divergence in a Californian paleoendemic: Sequoiadendron giganteum (giant sequoia)

Mediterranean ecosystems comprise a high proportion of endemic taxa whose response to climate change will depend on their evolutionary origins. In the California flora, relatively little attention has been given to the evolutionary history of paleoendemics from a molecular perspective, yet they number among some of the world's most iconic plant species. Here, we address questions of demographic change in Sequoiadendron giganteum (giant sequoia) that is restricted to a narrow belt of groves in the Sierra Nevada Mountains. We ask whether the current distribution is a result of northward colonization since the last glacial maximum (LGM), restriction of a broader range in the recent past (LGM) or independent colonizations in the deeper past. Genetic diversity at eleven microsatellite loci decreased with increasing latitude, but partial regressions suggested this was a function of smaller population sizes in the north. Disjunct populations north of the Kings River were divergent from those south of the Kings River that formed a single cluster in Bayesian assignment tests. Demographic inferences supported a demographic contraction just prior to the LGM as the most likely scenario for the current disjunct range of the species. This contraction appeared to be superimposed upon a long‐term decline in giant sequoia over the last 2 million years, associated with increasing aridity due to the Mediterranean climate. Overall, low genetic diversity, together with competition in an environment to which giant sequoia is likely already poorly adapted, will pose major constraints on its success in the face of increasing aridity.

Nuclear introgression without mitochondrial introgression in two turtle species exhibiting sex-specific trophic differentiation

Despite the presence of reproductive barriers between species, interspecific gene introgression has been documented in a range of natural systems. Comparing patterns of genetic introgression in biparental versus matrilineal markers can potentially reveal sex-specific barriers to interspecific gene flow. Hybridization has been documented in the freshwater turtles Graptemys geographica and G. pseudogeographica, whose ranges are largely sympatric. Morphological differentiation between the species is restricted to females, with female G. geographica possessing large heads and jaws compared to the narrow heads of G. pseudogeographica females. If hybrid females are morphologically intermediate, they may be less successful at exploiting parental feeding niches, thereby limiting the introgression of maternally inherited, but not biparental, molecular markers. We paired sequence data with stable isotope analysis and examined sex-specific genetic introgression and trophic differentiation in sympatric populations of G. geographica and G. pseudogeographica. We observed introgression from G. pseudogeographica into G. geographica at three nuclear loci, but not at the mitochondrial locus. Analysis of ∂(15)N and ∂(13)C was consistent with species differences in trophic positioning in females, but not males. These results suggest that ecological divergence in females may reduce the opportunity for gene flow in this system.

Development of microsatellite markers for Manilkara maxima T.D. Penn. (Sapotaceae) and their use in conservation genetics

Manilkara maxima is an endemic tree species of the Atlantic Forest in southern Bahia, Brazil. It is considered important for forest conservation due to its mutualistic interactions with endemic and endangered animals. Our aim was to develop microsatellite markers to estimate genetic diversity in order to provide information for effectiveness of future conservation programs. We used next generation sequencing technology to develop the first specific microsatellite markers for M. maxima. Seventeen new microsatellite loci were applied in 72 individuals sampled in three natural populations. On average, the number of alleles per loci was 8.8. The expected heterozygosity varied between 0.72 and 0.77, indicating that the developed set of molecular markers is useful for genetic diversity studies. Additionally, the estimated value for the combined probability of exclusion (Q) was greater than 0.999, which indicates the powerful of these molecular tools for paternity and kinship analysis. Our results demonstrate that the set of microsatellites developed in this work is a powerful tool for population genetics, molecular ecology and conservation biology purposes.

Fine scale patterns of genetic partitioning in the rediscovered African crocodile, Crocodylus suchus (Saint-Hilaire 1807)

Landscape heterogeneity, phylogenetic history, and stochasticity all influence patterns of geneflow and connectivity in wild vertebrates. Fine-scale patterns of genetic partitioning may be particularly important for the sustainable management of widespread species in trade, such as crocodiles. We examined genetic variation within the rediscovered African crocodile, Crocodylus suchus, across its distribution in West and Central Africa. We genotyped 109 individuals at nine microsatellite loci from 16 sampling localities and used three Bayesian clustering techniques and an analysis of contemporary gene flow to identify population structure across the landscape. We identified up to eight genetic clusters that largely correspond to populations isolated in coastal wetland systems and across large distances. Crocodile population clusters from the interior were readily distinguished from coastal areas, which were further subdivided by distance and drainage basin. Migration analyses indicated contemporary migration only between closely positioned coastal populations. These findings indicate high levels of population structure throughout the range of C. suchus and we use our results to suggest a role for molecular tools in identifying crocodile conservation units for this species. Further research, including additional sampling throughout the Congo and Niger drainages, would clarify both the landscape connectivity and management of this species.

Hybrid origin of European Vipers (Vipera magnifica and Vipera orlovi) from the Caucasus determined using genomic scale DNA markers

Background

Studying patterns of introgression can illuminate the role of hybridization in speciation, and help guide decisions relevant to the conservation of rare taxa. Vipera magnifica and Vipera orlovi are small vipers that have high conservation status due to their rarity and restricted distributions in an area of the Caucasus region where two other related species are present – V. kaznakovi and V. renardi. Despite numerous observations of hybridization between different species of small vipers, and the potential of a hybrid origin for V. magnifica and V. orlovi based on their distribution with respect to V. kaznakovi and V. renardi, hypotheses of a hybrid origin have not been formally tested. Here we generate genomic-scale data by performing next generation sequencing of double digest restriction-site associated DNA libraries, and use these multilocus data to test whether these two species are of hybrid origin.

Results

We generated over nine hundred loci for 38 specimens of six taxa, and analysed the dataset using Bayesian clustering and multivariate methods, as well as Patterson D-statistics, which can distinguish between incomplete lineage sorting and introgression as explanations for shared polymorphism. The results demonstrate a pattern of historical admixture in the two purported hybrids that is consistent with past gene flow from V. renardi into V. kaznakovi. The average admixture proportion in individuals was low (6.39 %) in the case of V. magnifica, but was higher in V. orlovi (19.02 %). We also show that the specific individual samples used in D-statistic tests can have a significant impact on inferences regarding the magnitude of introgression, suggesting the importance of including multiple individuals in these analyses.

Conclusions

Our results support the conclusion that both V. orlovi and V. magnifica had formed through a hybridization event between V. kaznakovi and V. renardi. Given a low proportion of admixture and absence of clear ecological and morphological differences V. magnifica should be treated as a marginal population of V. kaznakovi. Further studies that include analyses of ecological segregation of V. orlovi from parental taxa and search for evolutionary consequences of hybridisation would clarify if V. orlovi is a distinct hybrid species. Until this we recommend preserving the current taxonomy and protection status of V. orlovi.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0647-7) contains supplementary material, which is available to authorized users.

Genetic architecture and mechanism of seed number per pod in rapeseed: elucidated through linkage and near-isogenic line analysis

Seed number per pod (SNPP) is one of the major yield components and breeding targets in rapeseed that shows great variation and is invaluable for genetic improvement. To elucidate the genetic architecture and uncover the mechanism of SNPP, we identified five quantitative trait loci (QTLs) using the BnaZNRIL population, which were integrated with those of previous studies by physical map to demonstrate a complex and relatively complete genetic architecture of SNPP. A major QTL, qSN.A6, was successfully fine-mapped from 1910 to 267 kb using near-isogenic line (NIL). In addition, qSN.A6 exhibited an antagonistic pleiotropy on seed weight (SW), which is caused by a physiological interaction in which SNPP acts "upstream" of SW. Because the negative effect of qSN.A6 on SW cannot fully counteract its positive effect on SNPP, it also enhanced the final yield (17.4%), indicating its great potential for utilization in breeding. The following genetic and cytological experiments further confirmed that the different rate of ovule abortion was responsible for the ~5 seed difference between Zhongshuang11 and NIL-qSN.A6. This systematic approach to dissecting the comprehensive genetic architecture of SNPP and characterizing the underlying mechanism has advanced the understanding of SNPP and will facilitate the development of high-yield cultivars.

Revision of widespread red squirrels (genus: Tamiasciurus) highlights the complexity of speciation within North American forests

Integration of molecular methods, ecological modeling, and statistical hypothesis testing are increasing our understanding of differentiation within species and phylogenetic relationships among species by revealing environmental connections to evolutionary processes. Within mammals, novel diversity is being discovered and characterized as more complete geographic sampling is coupled with newer multi-disciplinary approaches. North American red squirrels exemplify a forest obligate genus whose species are monitored as indicators of forest ecosystem condition, yet phylogenetic relationships reflecting evolutionary history within this genus remain tentative. Through testing of competing systematic and niche-based divergence hypotheses, we recognize three species, Tamiasciurus douglasii, T. hudsonicus, and T. fremonti. Our data provide evidence of regional differences in evolutionary dynamics and continental gradients of complexity that are important both for future management and for investigating multiple pathways that can lead to the formation of new species.

Beyond animals and plants: dynamic maternal effects in the fungus Neurospora crassa

Maternal effects are widely documented in animals and plants, but not in fungi or other eukaryotes. A principal cause of maternal effects is asymmetrical parental investment in a zygote, creating greater maternal vs. paternal influence on offspring phenotypes. Asymmetrical investments are not limited to animals and plants, but are also prevalent in fungi and groups including apicomplexans, dinoflagellates and red algae. Evidence suggesting maternal effects among fungi is sparse and anecdotal. In an experiment designed to test for maternal effects across sexual reproduction in the model fungus Neurospora crassa, we measured offspring phenotypes from crosses of all possible pairs of 22 individuals. Crosses encompassed reciprocals of 11 mating-type 'A' and 11 mating-type 'a' wild strains. After controlling for the genetic and geographic distances between strains in any individual cross, we found strong evidence for maternal control of perithecia (sporocarp) production, as well as maternal effects on spore numbers and spore germination. However, both parents exert equal influence on the percentage of spores that are pigmented and size of pigmented spores. We propose a model linking the stage-specific presence or absence of maternal effects to cellular developmental processes: effects appear to be mediated primarily through the maternal cytoplasm, and, after spore cell walls form, maternal influence on spore development is limited. Maternal effects in fungi, thus far largely ignored, are likely to shape species' evolution and ecologies. Moreover, the association of anisogamy and maternal effects in a fungus suggests maternal effects may also influence the biology of other anisogamous eukaryotes.

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and both beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Hence, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift.

Biogeographic patterns provide insight into the evolutionary and ecological processes that govern biodiversity. However, the evolutionary and ecological processes that govern terrestrial microbial diversity remain poorly characterized. We evaluated the biogeography of the genus Streptomyces to show that the diversity of terrestrial bacteria is governed by many of the same processes that govern the diversity of many plant and animal species. While bacteria of the genus Streptomyces are a preeminent source of antibiotics, their evolutionary history, biogeography, and biodiversity remain poorly characterized. The observations we describe provide insight into the drivers of Streptomyces biodiversity and the processes that underlie microbial diversification in terrestrial habitats.

CRISPR/Cas9: A Tool to Circumscribe Cotton Leaf Curl Disease

The begomoviruses (family Geminiviridae) associated with cotton leaf curl disease (CLCuD) pose a major threat to cotton productivity in South-East Asia including Pakistan and India. These viruses have single-stranded, circular DNA genome, of ∼2800 nt in size, encapsidated in twinned icosa-hedera, transmitted by ubiquitous whitefly and are associated with satellite molecules referred to as alpha- and betasatellite. To circumvent the proliferation of these viruses numerous techniques, ranging from conventional breeding to molecular approaches have been applied. Such devised strategies worked perfectly well for a short time period and then viruses relapse due to various reasons including multiple infections, where related viruses synergistically interact with each other, virus proliferation and evolution. Another shortcoming is, until now, that all molecular biology approaches are devised to control only helper begomoviruses but not to control associated satellites. Despite the fact that satellites could add various functions to helper begomoviruses, they remain ignored. Such conditions necessitate a very comprehensive technique that can offer best controlling strategy not only against helper begomoviruses but also their associated DNA-satellites. In the current scenario clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR associated nuclease 9 (Cas9) has proved to be versatile technique that has very recently been deployed successfully to control different geminiviruses. The CRISPR/Cas9 system has been proved to be a comprehensive technique to control different geminiviruses, however, like previously used techniques, only a single virus is targeted and hitherto it has not been deployed to control begomovirus complexes associated with DNA-satellites. Here in this article, we proposed an inimitable, unique, and broad spectrum controlling method based on multiplexed CRISPR/Cas9 system where a cassette of sgRNA is designed to target not only the whole CLCuD-associated begomovirus complex but also the associated satellite molecules.

Post-mortem findings in southern right whales Eubalaena australis at Península Valdés, Argentina, 2003-2012

Between 2003 and 2012, 605 southern right whales (SRW; Eubalaena australis) were found dead along the shores of Península Valdés (PV), Argentina. These deaths included alarmingly high annual losses between 2007 and 2012, a peak number of deaths (116) in 2012, and a significant number of deaths across years in calves-of-the-year (544 of 605 [89.9%]; average = 60.4 yr(-1)). Post-mortem examination and pathogen testing were performed on 212 whales; 208 (98.1%) were calves-of-the-year and 48.0% of these were newborns or neonates. A known or probable cause of death was established in only a small number (6.6%) of cases. These included ship strike in a juvenile and blunt trauma or lacerations (n = 5), pneumonia (n = 4), myocarditis (n = 2), meningitis (n = 1), or myocarditis and meningitis (n = 1) in calves. Ante-mortem gull parasitism was the most common gross finding. It was associated with systemic disease in a single 1-2 mo old calf. Immunohistochemical labeling for canine distemper virus, Toxoplasma gondii and Brucella spp., and PCR for cetacean morbillivirus (CeMV), influenza A, and apicomplexan protozoa were negative on formalin-fixed, paraffin-embedded lung and brain samples from a subset of whales; PCR for Brucella spp. was positive in a newborn/neonate with pneumonia. Skin samples from whales with gull parasitism were PCR negative for CeMV, poxvirus, and papillomavirus. This is the first long-term study to investigate and summarize notable post-mortem findings in the PV SRW population. Consistent, significant findings within or between years to explain the majority of deaths and those in high-mortality years remain to be identified.

Little or no gene flow despite F1 hybrids at two interspecific contact zones

Hybridization can create the selective force that promotes assortative mating but hybridization can also select for increased hybrid fitness. Gene flow resulting from hybridization can increase genetic diversity but also reduce distinctiveness. Thus the formation of hybrids has important implications for long‐term species coexistence. This study compares the interaction between the tree wētā Hemideina thoracica and its two neighboring species; H. crassidens and H. trewicki. We examined the ratio of parent and hybrid forms in natural areas of sympatry. Individuals with intermediate phenotype were confirmed as first generation hybrids using nine independent genetic markers. Evidence of gene flow from successful hybridization was sought from the distribution of morphological and genetic characters. Both species pairs appear to be largely retaining their own identity where they live in sympatry, each with a distinct karyotype. Hemideina thoracica and H. trewicki are probably reproductively isolated, with sterile F₁ hybrids. This species pair shows evidence of niche differences with adult size and timing of maturity differing where Hemideina thoracica is sympatric with H. trewicki. In contrast, evidence of a low level of introgression was detected in phenotypes and genotypes where H. thoracica and H. crassidens are sympatric. We found no evidence of size divergence although color traits in combination with hind tibia spines reliably distinguish the two species. This species pair show a bimodal hybrid zone in the absence of assortative mating and possible sexual exclusion by H. thoracica males in the formation of F₁ hybrids.

Phylogenomic analyses reveal novel relationships among snake families

Snakes are a diverse and important group of vertebrates. However, relationships among the major groups of snakes have remained highly uncertain, with recent studies hypothesizing very different (and typically weakly supported) relationships. Here, we address family-level snake relationships with new phylogenomic data from 3776 nuclear loci from ultraconserved elements (1.40million aligned base pairs, 52% missing data overall) sampled from 29 snake species that together represent almost all families, a dataset ∼100 times larger than used in previous studies. We found relatively strong support from species-tree analyses (NJst) for most relationships, including three largely novel clades: (1) a clade uniting the boas, pythons and their relatives, (2) a clade placing cylindrophiids and uropeltids with this clade, and (3) a clade uniting bolyeriids (Round Island boas) with pythonids and their relatives (xenopeltids and loxocemids). Relationships among families of advanced snakes (caenophidians) were also strongly supported. The results show the potential for phylogenomic analyses to resolve difficult groups, but also show a surprising sensitivity of the analyses to the inclusion or exclusion of outgroups.

Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation

Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs), Eastern Asia (EAs), and Western Africa (WAf) were highly diversified, while those from Western Asia (WAs), Northern Africa (NAf), and Southeastern Africa (SAf) had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions.

Geographic variation in advertisement calls of a Microhylid frog - testing the role of drift and ecology

Acoustic signals for mating are important traits that could drive population differentiation and speciation. Ecology may play a role in acoustic divergence through direct selection (e.g., local adaptation to abiotic environment), constraint of correlated traits (e.g., acoustic traits linked to another trait under selection), and/or interspecific competition (e.g., character displacement). However, genetic drift alone can also drive acoustic divergence. It is not always easy to differentiate the role of ecology versus drift in acoustic divergence. In this study, we tested the role of ecology and drift in shaping geographic variation in the advertisement calls of Microhyla fissipes. We examined three predictions based on ecological processes: (1) the correlation between temperature and call properties across M. fissipes populations; (2) the correlation between call properties and body size across M. fissipes populations; and (3) reproductive character displacement (RCD) in call properties between M. fissipes populations that are sympatric with and allopatric to a congener M. heymonsi. To test genetic drift, we examined correlations among call divergence, geographic distance, and genetic distance across M. fissipes populations. We recorded the advertisement calls from 11 populations of M. fissipes in Taiwan, five of which are sympatrically distributed with M. heymonsi. We found geographic variation in both temporal and spectral properties of the advertisement calls of M. fissipes. However, the call properties were not correlated with local temperature or the callers' body size. Furthermore, we did not detect RCD. By contrast, call divergence, geographic distance, and genetic distance between M. fissipes populations were all positively correlated. The comparisons between phenotypic Q_st (P_st) and F_st values did not show significant differences, suggesting a role of drift. We concluded that genetic drift, rather than ecological processes, is the more likely driver for the geographic variation in the advertisement calls of M. fissipes.