Extensive Intraspecific Variation Research Articles

A new semi-fossorial thescelosaurine dinosaur from the Cenomanian-age Mussentuchit Member of the Cedar Mountain Formation, Utah.

Thescelosaurines are a group of early diverging, ornithischian dinosaurs notable for their conservative bauplans and mosaic of primitive features. Although abundant within the latest Cretaceous ecosystems of North America, their record is poor to absent in earlier assemblages, leaving a large gap in our understanding of their evolution, origins, and ecological roles. Here we report a new small bodied thescelosaurine-Fona herzogae gen. et sp. nov.-from the Mussentuchit Member of the Cedar Mountain Formation, Utah, USA. Fona herzogae is represented by multiple individuals, representing one of the most comprehensive skeletal assemblages of a small bodied, early diverging ornithischian described from North America to date. Phylogenetic analysis recovers Fona as the earliest member of Thescelosaurinae, minimally containing Oryctodromeus, and all three species of Thescelosaurus, revealing the clade was well-established in North America by as early as the Cenomanian, and distinct from, yet continental cohabitants with, their sister clade, Orodrominae. To date, orodromines and thescelosaurines have not been found together within a single North American ecosystem, suggesting different habitat preferences or competitive exclusion. Osteological observations reveal extensive intraspecific variation across cranial and postcranial elements, and a number of anatomical similarities with Oryctodromeus, suggesting a shared semi-fossorial lifestyle.

Intraspecific trait variation modulates the temperature effect on elemental quotas and stoichiometry in marine Synechococcus.

Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions, and we demonstrate contains extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in serially transferred cultures across a range of temperatures (16-25°C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We report differences in cell size (p<0.01) as a function of strain and clade (p<0.01). The carbon (QC), nitrogen (QN), and phosphorus (QP) cell quotas all increased with cell size. Furthermore, cell size has an inverse relationship to growth rate. Within our experimental design, temperature alone had a weak physiological effect on cell quota and elemental ratios. Instead, we find systemic intraspecific variance of C:N:P, with cell size and N:P having an inverse relationship. Our results suggest a key role for intraspecific life history traits in determining elemental quotas and stoichiometry. Thus, the extensive biodiversity harbored within many lineages may modulate the impact of environmental change on ocean biogeochemical cycles.

Comparative genomics of Lactobacillus johnsonii reveals extensive intraspecific genetic variation

Lactobacillus johnsonii, as a microorganism widely presenting in the intestinal tract of mammals, dairy products, and poultry, possesses various probiotic characteristics. Currently, many research focused on the probiotic functions and industrial applications of L. johnsonii. In this study, 98 strains of L. johnsonii were subjected to comparative genomic analyses to explore its genetic diversity. The results indicated that based on ANI values, d-DDH values, phylogenetic analysis, and whole-genome comparison, the 98 strains of L. johnsonii were classified into two phylogenetic clusters. The carbohydrate utilization genes, bacteriocin operon, extracellular polysaccharide gene cluster, and bile salt hydrolase encoding genes in L. johnsonii shared common features and exhibited systematic differences based on phylogenetic clustering. The main reason for the high intra-species gene diversity of L. johnsonii might be differences in phages and other mobile genetic elements. This study provides new insights into the genomic features and functional genes of L. johnsonii.

Modelling migration in birds: competition's role in maintaining individual variation.

Animals exhibit extensive intraspecific variation in behaviour. Causes of such variation are less well understood. Here, we ask when competition leads to the maintenance of multiple behavioural strategies. We model variability using the timing of bird migration as an example. Birds often vary in when they return from non-breeding grounds to establish breeding territories. We assume that early-arriving birds (counting permanent residents as 'earliest') select the best territories. But arriving before the optimal (frequency-independent) breeding date incurs a fitness penalty. Using simulations, we find stable sets of return dates. When year-round residency is viable, the greatest between-individual variation occurs when a small proportion of permanent residents is favoured, and the rest of the population varies in their return times. However, when fitness losses due to year-round residency exceed the benefits of breeding in the worst territory, all individuals migrate, although their return dates often vary continuously. In that case, individual variation is inversely related to fitness risks and positively related to territory inequality. This result is applicable across many systems: when there is more to gain through competition, or when its risks are small, a diversity of individual strategies prevails. Additionally, stability can depend upon the distribution of resources.

Weak directional selection on inducible defensive shell traits in a marine gastropod by the inducing shell-breaking predator

Predation can drive variation in prey phenotypes by selecting for both constitutive and inducible defensive traits, which can act in concert to protect prey from predators. To understand the adaptive evolution of prey traits it is important to determine which traits are true targets of natural selection. Selection gradient analysis is a useful tool for doing this. We combined field surveys of the extensive intraspecific variation in defensive shell traits of the intertidal whelk Nucella lamellosa with laboratory experiments to determine which traits were associated with risk of crab predation, and which traits were under selection by the whelks’ major crab predator, Cancer productus. Field surveys showed strong associations between risk of crab predation and shell shape, shell thickness, and apertural area, but not apertural teeth. Laboratory choice experiments in which crabs were offered a variety of whelk shell morphs revealed that thinner–shelled whelks with wider apertures were consumed significantly more often than thicker–shelled whelks with narrower apertures, confirming previous findings, and resulting in positive selection differentials for these traits. However, multiple logistic regression revealed that only shell thickness, and none of the other traits measured, had a significant effect on whelk survival, indicating only weak directional selection for this trait. The mechanism for crabs selecting for shell thickness in whelks is likely through increased handling time and decreased profitability. Given that shell thickness is a phenotypically plastic trait induced by C. productus, future work should examine the degree to which selection by crabs acts on both constitutive levels and inducibility of shell thickness in N. lamellosa.

Vanewrightia gen. nov.—A Highly Variable Taxon of Neotropical Ctenuchina (Lepidoptera: Erebidae: Arctiinae: Arctiini) Revealed by Behavioral Traits

Abstract A series of different-looking tiger moths was collected at pyrrolizidine alkaloid baits in the daytime in Peru. They proved to be variants of a new genus, Vanewrightia gen. nov., and a new species, Vanewrightia kiesela sp. nov., both described here. This species presents a striking example of extensive intraspecific variation within a population. Its discovery demonstrates the importance of sampling moths by means other than collecting with light, of studying patterns of wing undersides, and of the value of barcoding. Specimens found in collections considered here potentially to represent further species of the new genus are documented and discussed; Vanewrightia subflavescens (Kaye, 1911) comb. nov., and Vanewrightia patawaensis (Cerda, 2017) comb. nov. are established; we propose Epidesma parva (Rothschild, 1912) as a junior synonym of E. aurimacula (Schaus, 1905). The newly recognized intraspecific variation greatly challenges delimitation of morphospecies and uncovers uncertainties in the taxonomy of Epidesma Hübner, [1819]. The occurrence of an oblique forewing band in many Lepidoptera and the stunning similarity in overall appearance of variants of Vanewrightia with unrelated taxa, in particular notodontid moths (Josiini) and Chamaelimnas C. &amp; R. Felder, [1885] butterflies (Riodinidae), are discussed in the context of mimicry and crypsis, and some perspectives for further research are suggested.

Comparative genome analysis on intraspecific evolution and nitrogen fixation of Leptospirillum ferriphilum isolates

Abstract To reveal the intraspecific evolution of Leptospirillum ferriphilum isolates which thrived in industrial bioleaching ecosystems and acid mine drainages, genome sequences of L. ferriphilum YSK, L. ferriphilum DX and L. ferriphilum ZJ were determined to compare with complete genome of L. ferriphilum ML-04. The genome comparisons reveal that extensive intraspecific variation occurs in their genomes, and that the loss and insertion of novel gene blocks of probable phage origin may mostly contribute to heterogeneity of gene content among L. ferriphilum genomes. Surprisingly, a nif gene cluster is identified in L. ferriphilum YSK and L. ferriphilum ZJ genomes. Intensive analysis and further experiments indicate that the nif gene cluster in L. ferriphilum YSK inherits from ancestor rather than lateral gene transfer. Overall, results suggest that the population of L. ferriphilum undergoes frequent genetic recombination, resulting in many closely related genome types in recent evolution. The combinatorial processes profoundly shape their physiologies and provide the basis for adaptation to different niches.

Circular RNAs exhibit extensive intraspecific variation in maize

Comprehensive transcriptome profiling uncovers extensive intraspecific variation of circular RNAs in maize, shedding light on genomic and phenotypic variation among maize inbred lines. Circular RNAs (circRNAs) are single-strand, covalently closed transcripts. A substantial number of circRNAs have been identified and shown to be associated with phenotypic variation in various species. However, little is known about the intraspecific variation of circRNAs in maize (Zea mays L.). Here, we collected a large transcriptomic dataset (by circRNA-seq and mRNA-seq) from seedling leaves of the reference maize inbred lines B73 and Mo17. We identified over 1500 circRNAs in these lines using two circRNA detection methods, CIRCexplorer2 and CIRI. Notably, a substantial proportion of circRNAs varied in terms of sequence or expression level between lines, pointing to extensive intraspecific variation of circRNAs in maize. GO and KEGG analyses showed that genes producing circRNAs with intraspecific variation were more likely to be enriched in multiple functional groups, compared with those that did not produce circRNAs. These findings suggest that circRNAs could be utilized as an indicator of genomic and phenotypic variation among maize inbred lines. Ribosomal profiling revealed that several circRNAs might have translational capacity in maize. These results uncover the extensive intraspecific variation of circRNAs and pave the way for further understanding the molecular mechanisms underlying phenotypic variation at the circRNA level in maize.

Lamellose Axial Shell Sculpture Reduces Gastropod Vulnerability to Sea Star Predation.

Marine gastropods exhibit a stunning diversity of shell sculpture, but the functional significance of many sculpture types remains unknown. Unfortunately, experimental tests of the functional significance of differences between species are complicated by other morphological differences, such as shell microstructure, aperture shape, and shell thickness, that may confound interpretation. The most robust experimental tests are therefore performed using different shell forms within a species. We took advantage of the extensive intraspecific shell variation in the common intertidal gastropod Nucella lamellosa to test the adaptive significance of axial lamellae, a type of shell sculpture found in numerous marine gastropod subfamilies. We offered three forms of N. lamellosa (lamellose, artificially smooth, and naturally smooth) to the predatory sea star Pisaster ochraceus under controlled laboratory conditions. Pisaster ochraceus consumed significantly fewer lamellose snails than either artificially or naturally smooth snails. We suggest that shell lamellae deter sea star predation by impairing their ability to capture or manipulate snail prey or by increasing prey effective size. These results suggest a credible hypothesis for the adaptive significance of lamellar sculpture in marine gastropods and provide a valuable missing piece to the story about adaptive phenotypic plasticity in N. lamellosa shell form.

Cracking the Code: Examination of Species Delimitations amongHamadryasButterflies with DNA Barcodes Suggests Caribbean Cracker isHamadryas februaHübner (Nymphalidae: Biblidinae)

Hamadryas februa Hubner and close relatives H. amphichloe Boisduval, H. glauconome Bates and H. julitta Fruhstorfer are a homogeneous group of taxa loosely defined as different species mainly by a combination of wing color characters. Here we explored the utility of the mtDNA COI barcode region in delimiting these taxa and examined its overall performance to identify species of Hamadryas. We compiled all the barcode sequences available for 16 of the 20 species in the genus, and added new sequences from 34 samples for 8 species from Peru and Ecuador. The complete data set includes 260 individuals. After filtering out identical sequences, a parsimony analysis of 142 individuals with unique haplotypes found that almost all the samples grouped according to their traditional species identification. The exceptions were samples of H. amphichloe diasia Fruhstorfer from the Dominican Republic and H. amphichloe ferox Staudinger from Colombia, which grouped with samples of H. februa. The barcodes of widespread species or polytypic species such as H. laodamia Cramer, H. arinome Lucas and H. februa grouped according to the geographic limits of their subspecies, but this was not the case for H. amphichloe, H. feronia Linnaeus, H. amphinome Linnaeus and H. guatemalena Bates. Our results suggest that of the three subspecies of H. amphichloe included here, only H. amphichloe amphichloe Boisduval, originally described from Ecuador, should be considered a distinct species, and that H. amphichloe diasia and H. amphichloe ferox do not belong to that lineage, but instead are part of H. februa. Furthermore we found extensive intraspecific sequence variation that overlapped with interspecific genetic distances of closely related species. We offer some general comments on species delimitation by tree-based and distance-based approaches. In conclusion, our dataset shows that the majority of the species Hamadryas included here can be distinguished by their barcode sequence (11 of 16 or about half of the species in the genus). However, the geographical coverage of our dataset is somewhat limited. Broader sampling of widespread species and the comprehensive inclusion of samples from closely related species will determine the utility of the barcode with more confidence.

Social structure affects mating competition in a damselfish

The strength of mating competition and sexual selection varies over space and time in many animals. Such variation is typically driven by ecological and demographic factors, including adult sex ratio and consequent availability of mates. The spatial scale at which demographic factors affect mating competition and sexual selection may vary but is not often investigated. Here, we analyse variation in size and sex ratio of social groups, and how group structure affects mating competition, in the site-attached damselfish Chrysiptera cyanea. Site-attached reef fishes are known to show extensive intraspecific variation in social structure. Previous work has focused on species for which the size and dynamics of social groups are constrained by habitat, whereas species with group structure unconstrained by habitat have received little attention. Chrysiptera cyanea is such a species, with individuals occurring in spatial clusters that varied widely in size and sex ratio. Typically, only one male defended a nest in multi-male groups. Nest-holding males were frequently visited by mate-searching females, with more visits in groups with more females, suggesting that courtship and mating mostly occur within groups and that male mating success depends on the number of females in the group. Male–male aggression was frequent in multi-male groups but absent in single-male groups. These findings demonstrate that groups are distinct social units. In consequence, the dynamics of mating and reproduction are mainly a result of group structure, largely unaffected short term by overall population demography which would be important in open social systems. Future studies of the C. cyanea model system should analyse longer-term dynamics, including how groups are formed, how they vary in relation to density and time of season and how social structure affects sexual selection.

Classification of intra-specific variation in plant functional strategies reveals adaptation to climate.

In plants, extensive intra-specific variation exists in the allocation of resources between vegetative growth and reproduction, reflecting different functional strategies. A simple method for the classification of intra-specific variation in these strategies would enable characterization of evolutionary and ecological processes. C-S-R theory can be applied to classify functional strategies (competitive C; stress tolerant, S; ruderal, R) in different plant species. Using a diverse set of arabidopsis ( Arabidopsis thaliana ) accessions grown under common conditions, it was tested whether a simple approach designed for allocating C-S-R strategies at the species level can also be used to analyse intra-specific variation. Substantial intra-specific variation between arabidopsis accessions was found along the S-R axis. There was a positive correlation of temperature at the geographical origin with the dimension of S and a negative correlation with the dimension of R. Flowering time in a natural annual cycle and leaf dry matter content were identified as the main determinants of this adaptation, with plants originating from warmer climates having a higher leaf dry matter content and flowering earlier in a common garden. It was shown that functional strategies reflect adaptation to climate, with consequences for important traits such as fecundity and total plant dry weight. The approach could be used in genome-wide association studies to determine the genetic basis of functional strategies in wild species or crops.

A below-ground herbivore shapes root defensive chemistry in natural plant populations.

Plants display extensive intraspecific variation in secondary metabolites. However, the selective forces shaping this diversity remain often unknown, especially below ground. Using Taraxacum officinale and its major native insect root herbivore Melolontha melolontha, we tested whether below-ground herbivores drive intraspecific variation in root secondary metabolites. We found that high M. melolontha infestation levels over recent decades are associated with high concentrations of major root latex secondary metabolites across 21 central European T. officinale field populations. By cultivating offspring of these populations, we show that both heritable variation and phenotypic plasticity contribute to the observed differences. Furthermore, we demonstrate that the production of the sesquiterpene lactone taraxinic acid β-D-glucopyranosyl ester (TA-G) is costly in the absence, but beneficial in the presence of M. melolontha, resulting in divergent selection of TA-G. Our results highlight the role of soil-dwelling insects for the evolution of plant defences in nature.

Hypnea musciformis (Cystocloniaceae) from the Yucatan Peninsula: morphological variability in relation to life-cycle phase

:Hypnea musciformis is one of the most studied species of the genus Hypnea. It has a wide geographic range along the Atlantic, Pacific and Indian Oceans that would be consistent with an extensive intraspecific variation in morphology. Hypnea musciformis has been previously reported on coasts of the Yucatan Peninsula; however, neither morphological characterization nor molecular studies have been done for Gulf of Mexico or Mexican Caribbean populations. For the first time, we present a detailed morphoanatomical description of the tetrasporophytic, gametophytic and carposporophytic phases and its reproductive structures for this region, including the description of the male gametophyte. Mexican Caribbean samples showed morphological variation in branching pattern, branch abundance and branchlet types, and this was attributed to life-history phase and the reproductive status of the thalli. Molecular analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase gene and the 5′ region of the mitochondrial cytochrome C oxidase subunit I gene markers allows us to confirm the unique genetic identity of Mexican specimens. The analysis of H. musciformis collected in different tropical areas showed a high degree of intraspecific variation and suggested the necessity of a combined analysis of morphology and different gene markers for a better understanding of its taxonomy and phylogeny.

Contrasting egg recognition between European and Asian populations of tree sparrows (Passer montanus)

Although many biological phenotypes are generally regarded as consistent across the distributional range of a species, some traits such as egg discrimination behavior have been shown to display extensive intraspecific variation as a response to selection from brood parasitism. We investigated the egg recognition ability in an Asian population of tree sparrows (Passer montanus), and we compared that with the ability to recognize and reject intraspecific foreign eggs in a population in Europe. Extensive artificial parasitism with model eggs and real eggs of eight sympatric birds that vary in background color and markings revealed that egg recognition capacity is completely absent in this Asian population of tree sparrows. This result contrasts with previous studies in European populations showing extensive ability for discriminating between own and foreign eggs. Different evolutionary equilibria or differences in the risk of conspecific parasitism may account for differences in egg discrimination ability between European and Asian populations of tree sparrows.

An illustrated key to the cuckoo wasps (Hymenoptera, Chrysididae) of the Nordic and Baltic countries, with description of a new species.

The Chrysididae are a group of cleptoparasitic and parasitoid aculeate wasps with a large number of rare and endangered species. The taxonomy of this group has long been confusing due to the similarity of species and extensive intraspecific variation. We present for the first time a comprehensive dichotomous key for all 74 species found in the Nordic and Baltic countries. In addition to diagnostic characters, information on the distribution and biology of each species is also presented. A new species, Chrysis borealis Paukkunen, Ødegaard & Soon, sp. n. is described on the basis of specimens collected from Fennoscandia. Chrysis gracillima Förster, 1853 is recorded as new to the Nordic and Baltic countries.

A New Species ofCraugastor(Anura: Craugastoridae) from the Magdalena River Valley, Colombia, with Evaluation of the Characters Used to Identify Species of theCraugastor fitzingeriGroup

Abstract. The Craugastor fitzingeri group is composed of eight species, four of which occur in sympatry in Colombia: C. crassidigitus, C. fitzingeri, C. longirostris, and C. raniformis. These four species frequently are confused due to their external similarity and extensive intraspecific variation, particularly between the species with disjunct populations in the middle and upper Magdalena River Valley, Colombia. Here we present the results of a revision of the variation in the morphological characters used to distinguish these four species. We confirm that the color patterns on the rear of the thigh and the degree of foot webbing are useful for distinguishing among these species; however, the color pattern on the throat was found to present extensive intraspecific variation. We show that C. fitzingeri and C. longirostris are restricted to the Pacific lowlands and upper basins of the Cauca River Valley in Colombia and that populations in the Magdalena River Valley previously identified as those species c...

Mechanistic basis of adaptive maternal effects: egg jelly water balance mediates embryonic adaptation to acidity in Rana arvalis.

Environmental stress, such as acidification, can challenge persistence of natural populations and act as a powerful evolutionary force at ecological time scales. The ecological and evolutionary responses of natural populations to environmental stress at early life-stages are often mediated via maternal effects. During early life-stages, maternal effects commonly arise from egg coats (the extracellular structures surrounding the embryo), but the role of egg coats has rarely been studied in the context of adaptation to environmental stress. Previous studies on the moor frog Rana arvalis found that the egg coat mediated adaptive divergence along an acidification gradient in embryonic acid stress tolerance. However, the exact mechanisms underlying these adaptive maternal effects remain unknown. Here, we investigated the role of water balance and charge state (zeta potential) of egg jelly coats in embryonic adaptation to acid stress in three populations of R. arvalis. We found that acidic pH causes severe water loss in the egg jelly coat, but that jelly coats from an acid-adapted population retained more water than jelly coats from populations not adapted to acidity. Moreover, embryonic acid tolerance (survival at pH 4.0) correlated with both water loss and charge state of the jelly, indicating that negatively charged glycans influence jelly water balance and contribute to embryonic adaptation to acidity. These results indicate that egg coats can harbor extensive intra-specific variation, probably facilitated in part via strong selection on water balance and glycosylation status of egg jelly coats. These findings shed light on the molecular mechanisms of environmental stress tolerance and adaptive maternal effects.

Species status of Bombus monticola Smith (Hymenoptera: Apidae) supported by DNA barcoding.

Certain species of bumblebees are difficult to distinguish based on morphology alone due to a lack of diagnostic characters and extensive intraspecific variation in colour patterns. The discussion concerning whether Bombus lapponicus and Bombus monticola are the same species or not, seems to be ongoing. We present a study of 16 speciemens of B. monticola/B. lapponicus from Norway, identified with previously published morphological characters and with DNA barcoding. The results showed a match with the examination of the morphological characters and the DNA sequence data. These results confirm that B. lapponicus and B. monticola appear as separate species in Norway, which supports earlier conclusions based on both morphological differences and differences in cephalic marking pheromones in males. The wide sympatric range of the two taxa in Scandinavia also strongly support their species status.

Cryptic phenotypic plasticity in populations of the freshwater prosobranch snail, Pleurocera canaliculata

We sampled four populations of the robustly shelled Pleurocera canaliculata from large rivers and five pleurocerid populations bearing more fusiform shells (nominally P. acuta and P. pyrenellum) from smaller streams in a study area extending from upstate New York to northern Alabama, USA. Gene frequencies at 9 allozyme-encoding loci revealed that each population of P. acuta or P. pyrenellum was more genetically similar to the P. canaliculata population inhabiting the larger river immediately downstream than to any nominal conspecific. Thus, the extensive intraspecific variation in shell robustness displayed by these nine populations has apparently been rendered cryptic by taxonomic confusion. We then employed geometric morphometrics to explore a gradient in shell morphology from the acuta form to the typical canaliculata form in 18 historic samples collected down the length of Indiana’s Wabash River. The shell forms appeared generally distinctive on the major axes yielded by relative warp analysis (increasing robustness and decreasing spire elongation), although some overlap was apparent. MANCOVA returned a significant relationship between multivariate shape variation and stream size, as measured by drainage area. Possible drivers for this phenomenon include an environmental cline in the risk of dislodgement due to hydrodynamic drag and shifts in the community of predators.