The Middle Pleistocene hominin mandible from Payre (Ardèche, France).

Although Neandertals are the best-known fossil hominins, the tempo and evolutionary processes in their lineage are strongly debated. This is in part due to the scarcity of the fossil record, in particular before the marine isotopic stage (MIS) 5. In 2010, a partial hominin mandible was discovered at the Middle Paleolithic site of Payre (France) in a layer that is dated to the end of MIS 8/beginning of MIS 7, a time period for which very few fossils are known in Europe. The Payre 15 mandible retains the complete symphyseal region and right lateral corpus with heavily worn P4, M1, and M2 in situ. Taphonomic modifications in the form of three notches suggest that this individual was chewed by a carnivore. We provide here the first detailed description of this specimen and a comparative analysis that includes morphological features, linear mandibular dimensions, an elliptic Fourier analysis of the symphysis, and a morphometric analysis of the M1 roots (based on segmented CT scan data). Our comparative sample encompasses European Middle and Upper Pleistocene specimens attributed to Homo heidelbergensis and Homo neanderthalensis, Upper Pleistocene Homo sapiens, and Holocene Homo sapiens. The Payre 15 mandible shows a combination of primitive and Neandertal-like features, with a receding symphyseal profile without any element of the mentum osseum, a posterior location of the mental foramen and lateral prominence. Its mandibular body is tall and thick anteriorly. Payre 15 has mesotaurodont M1 roots and a three-rooted M2. By its dimensions and combination of features, Payre 15 aligns better with Middle Pleistocene European hominins than with MIS 6-3 Neandertals. Noteworthy, it falls well within the range of variation of the Sima de los Huesos sample. Our results underscore that the total pattern of Neandertal-derived morphology was not achieved at the beginning of the MIS 7 and suggest a low level of mandibular diachronic changes for the period MIS 11-7.

Unravelling the stock structure of the Persian brown trout by otolith and scale shape.

The simultaneous use of the scale and otolith morphometry was assessed as a potential tool for the identification of Persian brown trout Salmo trutta stocks of the Lar Lake and five rivers from Lar Basin, Iran. Fourier coefficients (FC) and circularity, rectangularity, roundness, ellipticity and form factor shape indices (SI) were calculated for otolith and scale. Several SIs were significantly different among sites for both structures. Permutational multivariate analysis of variance revealed significant differences between several pairwise comparisons for otolith and scale (FCs and indices separately). Discriminant analysis showed otolith FCs (cross-classification rates: 25-86%) and SI (20-45%) appear to be a relatively acceptable tool to discriminate between several locations. Comparatively, the scale morphometry showed lower discriminatory power (FC = 3-65%; SI = 15-34%), with the exception of SI for Elarm River (60%), Kamardasht River (56%) and Lar Lake (75%). Cross-classification rates improved up to 100% when discriminate analysis incorporating all variables for otolith and scale was performed. The results showed a potential segregation between some water bodies, suggesting that the otolith and scale morphometry could be a useful tool to delimit S. trutta populations in relatively close freshwater environments.

Genome-wide association analysis of host genotype and plastic wing morphological variation of an endoparasitoid wasp Asobara japonica (Hymenoptera: Braconidae).

Accumulating evidence suggests that genotype of host insects influences the development of koinobiont endoparasitoids. Although there are many potential genetic variations that lead to the internal body environmental variations of host insects, association between the host genotype and the parasitoid development has not been examined in a genome-wide manner. In the present study, we used highly inbred whole genome sequenced strains of Drosophila melanogaster to associate single nucleotide polymorphisms (SNPs) of host flies with morphological traits of Asobara japonica, a larval-pupal parasitoid wasp that infected those hosts. We quantified the outline shape of the forewings of A. japonica with two major principal components (PC1 and PC2) calculated from Fourier coefficients obtained from elliptic Fourier analysis. We also quantified wing size and estimated wasp survival. We then examined the association between the PC scores, wing size and 1,798,561 SNPs and  the association between the estimated wasp survival and 1,790,544 SNPs. As a result, we obtained 22, 24 and 14 SNPs for PC1, PC2 and wing size and four SNPs for the estimated survival with P values smaller than 10-5. Based on the location of the SNPs, 12, 17, 11 and five protein coding genes were identified as potential candidates for PC1, PC2, wing size and the estimated survival, respectively. Based on the function of the candidate genes, it is suggested that the host genetic variation associated with the cell growth and morphogenesis may influence the wasp's morphogenetic variation.

The characteristic mid-shaft cross-sectional shape of the ulna in Jomon hunter-gatherers.

OBJECTIVES: The Jomon people were hunter-gatherers who inhabited the Japanese archipelago between 10,000 BC and 300 BC. Here, we focus on the mid-shaft cross-sectional shape of the ulna in the Jomon population and compare it with modern Japanese people. MATERIALS AND METHODS: Jomon specimens, including 32 males and 22 females, were excavated from shell mound sites in the Pacific and Seto inland coastal area of Honshu island in the Japanese archipelago dated to the Late-to-Final Jomon phase (between 2,000 BC and 300 BC). Mid-shaft ulna cross-sectional shapes were compared with modern Japanese specimens (25 males, 21 females) using standard linear measurements and elliptic Fourier analysis (EFA). Differences from both sides of this element were compared using predicted handedness. RESULTS: Linear measurements and EFA results show that ulna shape of both sexes within the Jomon population are relatively larger in the antero-posterior direction and have more developed posterior borders than modern Japanese males and females. No significant differences were observed between Jomon sexes based on the predicted dominant side, but differences were evident in the predicted nondominant side. At the same time, bilateral differences were recognized in Jomon females, because of a lower level of posterior border development in the predicted nondominant side compared to the dominant side. DISCUSSION: Shape differences between Jomon people and modern Japanese can be explained by variation in the habitual loading of the ulna. Sexual dimorphism in ulna shape within the Jomon population suggests division of labor differences.

Geometric morphometrics for the taxonomy of 11 species of Anopheles (Nyssorhynchus) mosquitoes.

The subgenus Anopheles (Nyssorhynchus) (Diptera: Culicidae) includes the primary vectors of Plasmodium spp. in Colombia. Most adult females of this subgenus are difficult to identify in the field using the available keys. With the objective of further investigating the discriminatory power of modern morphometrics, both landmark-based and outline-based approaches were explored using the wing venation geometry of 11 Anopheles (Nyssorhynchus) species. Wing shape was able to separate the closest species of the subgenus. When the 11 species were analysed together, validated classification scores on average 5.3-8.6 times higher than those expected by chance were observed. These scores computed from the total sample of 11 species were not satisfactory for the recognition of Anopheles benarrochi B, Anopheles oswaldoi s.l. and Anopheles strodei. These sibling species were captured in sympatry. To improve the identification power of the morphometric tool, it was necessary to analyse these species separately from the remaining species. The best classification scores were obtained using a combination of 12 landmarks collected not only on the intersections of wing veins, but also on spots. An outline approach also gave excellent reclassification scores. Another pair of sibling species, collected in allopatry, Anopheles nuneztovari and Anopheles rangeli, also showed high classification scores.

Geometric morphometric anatomy of the lacrimal punctum in normal population: Punctum update (PUP) study - Paper 5.

BACKGROUND: To investigate the geometric morphological differences of the lacrimal punctum by analyzing its shape in relation to age and sex in a normal population. METHODS: 960 high-magnification slit-lamp images were obtained from 320 puncta of normal asymptomatic Indian individuals across eight decades of life. Using advanced geometric morphometric techniques, including Elliptic Fourier Analysis and Principal Component Analysis, the intricate details of the lacrimal punctum's shape in a diverse population sample were categorized by age and sex. High-resolution images of the lacrimal punctum underwent standardization for scale and orientation, followed by precise landmark identification and coordinate data extraction. RESULTS: The geometric morphometry of the lacrimal punctum shows significant changes as one ages. However, the gender differences, in isolation, without consideration of age, remain subtle and are not pronounced. Interestingly, detailed Principal Component scores analysis revealed potential sex- and age-related variations specifically for the left and right lower puncta, which warrant further investigation. These changes could reflect unique aging changes in the proximal lacrimal drainage system. CONCLUSION: The study is a starting point for geometric morphometric analysis of the lacrimal punctum and provides valuable insights into the punctal changes in size, orientation, and overall morphology across different age groups and between sexes. These findings highlight the significance of considering individual age-wise anatomical variations to better understand the lacrimal punctum.

Luminal shape and aortic remodelling after total arch replacement for type A aortic dissection: conventional and frozen elephant trunks.

OBJECTIVES: This study was performed to assess postoperative aortic remodelling (AR) after total arch replacement for acute type A aortic dissection (AAD) with a frozen elephant trunk (FET) or conventional elephant trunk (cET). Furthermore, the shape of the residual true lumen was analysed based on elliptical Fourier analysis and evaluated as a predictor of AR. METHODS: This study involved patients who underwent total arch replacement with a cET or FET for AAD from December 2006 to January 2023 at five institutions. AR was assessed at the levels of the 4th thoracic vertebra (Th4), Th7, Th10, and above the coeliac trunk. The shape of the residual true lumen at all four levels was analysed based on elliptical Fourier analysis to calculate shape patterns as principal component (PC) values. Inverse probability of treatment weighting was performed for adjustment between the groups. RESULTS: In total, 180 patients (88 with cET and 92 with FET) were enrolled. The complete AR rate, defined as false lumen remodelling throughout the entire descending thoracic aorta, was significantly higher in the FET than cET group (63.4% vs 32.0%, P = 0.0013). The inverse probability of treatment weighting-adjusted Fine-Gray regression model revealed that the mean PC2 (hazard ratio, 0.22; P < 0.001) and PC3 (hazard ratio, 0.24; P = 0.009) of the four levels were independent predictors of complete AR. CONCLUSIONS: In AAD repair, the AR rate was significantly higher with use of the FET than cET. The shape patterns of the residual true lumen can be an important reference for predicting postoperative AR.

A Novel Approach for the Shape Characterisation of Non-Melanoma Skin Lesions Using Elliptic Fourier Analyses and Clinical Images.

The early detection of Non-Melanoma Skin Cancer (NMSC) is crucial to achieve the best treatment outcomes. Shape is considered one of the main parameters taken for the detection of some types of skin cancer such as melanoma. For NMSC, the importance of shape as a visual detection parameter is not well-studied. A dataset of 993 standard camera images containing different types of NMSC and benign skin lesions was analysed. For each image, the lesion boundaries were extracted. After an alignment and scaling, Elliptic Fourier Analysis (EFA) coefficients were calculated for the boundary of each lesion. The asymmetry of lesions was also calculated. Then, multivariate statistics were employed for dimensionality reduction and finally computational learning classification was employed to evaluate the separability of the classes. The separation between malignant and benign samples was successful in most cases. The best-performing approach was the combination of EFA coefficients and asymmetry. The combination of EFA and asymmetry resulted in a balanced accuracy of 0.786 and an Area Under Curve of 0.735. The combination of EFA and asymmetry for lesion classification resulted in notable success rates when distinguishing between benign and malignant lesions. In light of these results, skin lesions' shape should be integrated as a fundamental part of future detection techniques in clinical screening.

Dorso-palmar elongation of the diaphysis of the third metacarpal bone in prehistoric Jomon people.

This study investigated cross-sectional morphological differences in the diaphysis of the third metacarpal bone (MC3) between prehistoric Jomon hunter-gatherers and modern Japanese people. Overall, 179 skeletal remains of 119 individuals (73 men and 46 women) from the Middle-to-Final Jomon period (3500 BC-500 BC) and 60 modern Japanese people (35 men and 25 women) were included in the analysis. Analyses were performed at the mid-shaft of the MC3 using linear measurement, elliptic Fourier analysis, and cross-sectional geometric properties. The standardized polar section modulus (ZpSTD) indicated sexual differences in both populations. The right MC3 was generally stronger than the left side. There was no populational difference in the ZpSTD in both sexes. In both men and women, the cross-sectional shape of the MC3 was relatively larger in the dorso-palmar direction than in the radioulnar direction in the Jomon population compared to the modern Japanese population. Sexual differences in cross-sectional shape were recognized only in the Jomon population, with the dorso-palmar elongation being greater in Jomon men than in women (particularly when comparing the left MC3). There was a significant side difference in the diaphyseal shape among Jomon women, with the right MC3 being relatively larger in the dorso-palmar direction. These findings were consistent, although skeletal remains of the Jomon population were excavated from different regions. Differences in the diaphyseal cross-sectional shape between populations suggest differences in habitual loading on MC3 associated with differences in subsistence behavior. Furthermore, differences in diaphyseal shape and strength between Jomon men and women suggest sexual division of labor, with men performing bimanual tasks and women performing unimanual tasks.

Multivariate Analysis Approaches for Dimension and Shape Discrimination of Vitis vinifera Varieties.

In this study, berry dimensions and shape traits, which are important for the design of the grape processing system and the classification of 10 different grape varieties grown in same ecological conditions ('Ata Sarisi', 'Baris', 'Dimiski', 'Hatun Parmagi', 'Helvani', 'Horoz Karasi', 'Hönüsü', 'Italia', 'Mevlana Sarisi', and 'Red Globe') were determined; differences between the varieties were identified with the use of discriminant analysis. The largest grape varieties were identified as 'Ata Sarisi' and 'Red Globe'. The 'Red Globe' and 'Helvani' varieties had geometrically sphere-like shape. The 'Baris' variety had the lowest size averages. According to elliptic Fourier analysis, the primary source of shape variation was ellipse and sphere-looking varieties. However, shape variation was seen due to the existence of a small number of drop-like varieties. According to discriminant analysis, shape differences of the varieties were defined by two discriminant functions. Based on these discriminant functions, the greatest classification performance was achieved for 'Mevlana Sarisi' and 'Dimiski'. In scatter plots, three shape definitions (sphere, ellipse, and drop) were made for grape varieties. Cluster analysis revealed 4 sub-groups. The first sub-group included the 'Mevlana Sarisi' variety; the second sub-group included the 'Hönüsü', 'Hatun Parmagi', 'Dimiski', and 'Horoz Karasi' varieties; the third sub-group included the 'Ata Sarisi' variety; the fourth sub-group included the 'Baris', 'Helvani', 'Italia', and 'Red Globe' varieties. The variety in the first group had a geometrically ellipse-like shape, the largest length, and the smallest width. The size data were the smallest for the second sub-group. The third sub-group, with the ellipse-like shape, had the large size data. The grape varieties the closest to the sphere were classified in the fourth group, and these varieties had the large sizes.

Species specificity and sexual dimorphism in tooth shape among the three sympatric haplochromine species in Lake Kivu cichlids.

Tooth shape is used to differentiate between morphologically similar species of vertebrates, including fish. This study aimed to quantify tooth shape of three sympatric species: Haplochromis kamiranzovu, H. insidiae, and H. astatodon endemic to Lake Kivu, whose existing identification criteria are currently only qualitative. A quantitative tooth shape analysis was performed based on digitized tooth outline data with a subsequent elliptic Fourier analysis to test for differences among the three species. We looked at crown shape and size differences within H. kamiranzovu and H. insidiae at geographical, habitat, and gender levels. No comparison at habitat level was done for H. astatodon because it is found only in littoral zone. The analysis revealed significant tooth shape differences among the three species. Haplochromis astatodon had a significantly longer major cusp height and a longer and larger minor cusp than that of H. insidiae. It had also a longer major cusp height and a longer and larger minor cusp than that of H. kamiranzovu. Tooth shape differences of H. kamiranzovu and H. insidiae species were not significantly different between littoral and pelagic fish (p > .05) while differences were significant between southern and northern Lake Kivu populations (p < .05). Tooth sizes in H. kamiranzovu and H. insidiae were significantly different, both in height and width as well as in their ratios, and this was true at sex and geographic levels (p < .05), but not at habitat level (p > .05). Tooth shape was also significantly different with sharp teeth for males compared with females of southern populations versus northern ones. These shape- and size-related differences between sexes suggest differences in the foraging strategies toward available food resources in the lake habitat. Further research should explain the genetic basis of the observed pattern.

Morphological predictor of remodelling of the descending thoracic aortic false lumen that remains patent after repair of acute type A dissection.

OBJECTIVES: Some patients achieve complete recovery through false lumen remodelling in the descending aorta after surgery for acute type A aortic dissection. Our goal was to investigate the relationship between false lumen remodelling during later postoperative stages and quantitative analysis of the true lumen shape during the early postoperative stages. METHODS: We examined 88 surgical patients between January 2007 and December 2016. Three points of the descending aorta were assessed from the 6th (T6), the 9th (T9) and the 11th (T11) vertebral levels. The shape of the true lumen was evaluated during the early postoperative stages, and false lumen remodelling 1 year after surgery was the end point. The parameters obtained by evaluating the shape of the true lumen comprised the first principal component analysis using elliptic Fourier analysis, the minor diameter ratio and the ratio of the area of the true lumen to that of the descending aorta, and the number of contact points on the true lumen wall during the early stages. RESULTS: Using univariate analysis, we detected significant differences in the first principal components, the minor diameter ratio, the area ratio and the number of contact points at each thoracic vertebral level (P < 0.05). The cut-off value of the minor diameter ratio was 0.55, and the area ratio was 0.48 as determined by analysis of the receiver operating characteristic. Multivariable logistic analysis indicated that the first principal component was the most significant predictor from the proximal to the middle descending aorta. CONCLUSIONS: Quantitative evaluation of shape of the true lumen in the early postoperative stages after surgery for acute type A dissection can serve as a viable predictor for false lumen remodelling in later stages. Furthermore, the first principal component could serve as a more astute predictor than other quantitative parameters according to multivariate analysis.

Allometric shell growth in infaunal burrowing bivalves: examples of the archiheterodonts Claibornicardia paleopatagonica (Ihering, 1903) and Crassatella kokeni Ihering, 1899.

We present two cases of study of ontogenetic allometry in outlines of bivalves using longitudinal data, a rarity among fossils, based on the preserved post-larval record of shells. The examples are two infaunal burrowing bivalves of the southern South America, Claibornicardia paleopatagonica (Archiheterodonta: Carditidae) (early Paleocene) and Crassatella kokeni (Archiheterodonta: Crassatellidae) (late Oligocene-late Miocene). Outline analyses were conducted using a geometric morphometric approach (Elliptic Fourier Analysis), obtaining successive outlines from shells' growth lines, which were used to reconstruct ontogenetic trajectories. In both taxa, ontogenetic changes are characterized by the presence of positive allometry in the extension of posterior end, resulting in elongated adult shells. This particular allometric growth is known in others infaunal burrowing bivalves (Claibornicardia alticostata and some Spissatella species) and the resulting adult morphology is present in representatives of several groups (e.g., Carditidae, Crassatellidae, Veneridae, Trigoniidae). Taxonomic, ecological and evolutionary implications of this allometric growth pattern are discussed.

Shape outline extraction software (DiaOutline) for elliptic Fourier analysis application in morphometric studies.

PREMISE OF THE STUDY: Studies of plant cell and organ outline using shape analysis for taxonomic and morphological research have increased in the past decade. However, there are a limited number of available modern, intuitive, and easy software tools to conduct this work. METHODS: We developed a tool for shape outline extraction using MATLAB accompanied with R scripts to perform elliptic Fourier analysis. To demonstrate the shape tool, we applied the software and scripts for genera and species shape determinations of diatom (single cell) species with x-, y-, and x- + y-shape symmetries. RESULTS: Using the shape analysis tool, we were able to identify and distinguish different diatom taxa based on forms representing size diminutions associated with population changes. DISCUSSION: Independent of symmetry, species were successfully distinguished using supervised and unsupervised analyses. We hope that these shape analysis tools will be used to add another metric to plant science studies.

Asymmetric larval head and mandibles of Hydrophilus acuminatus (Insecta: Coleoptera, Hydrophilidae): Fine structure and embryonic development.

The larvae of a water scavenger beetle, Hydrophilus acuminatus, have strongly asymmetric mandibles; the right one is long and slender, whereas the left one is short and stout. The fine structure and embryonic development of the head capsule and mandibles of this species were examined using light and scanning electron microscopy, and asymmetries in shape were detected in these structures applying an elliptic Fourier analysis. The larval mandibles are asymmetric in the following aspects: whole length, the number, structure and arrangement of retinacula (inner teeth), and size and shape of both the molar and incisor regions. The larval head is also asymmetric; the left half of the head capsule is larger than the right, and the left adductor muscle of the mandible is much thicker than the right. The origin and developmental process of asymmetric mandibles were traced in developing embryos whose developmental period is about 270 h and divided into 10 stages. Mandibular asymmetries are produced by the cumulative effects of six stepwise modifications that occur from about 36% of the total developmental time onward. The significance of these modifications was discussed with respect to the functional advantages of asymmetries and the phylogeny of members of the Hydrophilidae.

New predictor of aortic enlargement in uncomplicated type B aortic dissection based on elliptic Fourier analysis.

OBJECTIVES: This study aimed to re-examine the conventional predictive factors for dissected aortic enlargement, such as the aortic and false lumen diameter and to consider whether the morphological elements of the dissected aorta could be predictors by quantifying the 'shape' of the true lumen based on elliptic Fourier analysis. METHODS: A total of 80 patients with uncomplicated type B aortic dissection were included. The patients were divided into 'Enlargement group' and 'No Change group.' Between the 2 groups, the mean systolic blood pressure during follow-up, aortic and false lumen maximum diameters, and analysed morphological data were compared using each statistical method. RESULTS: The maximum aortic and false lumen diameters were significantly larger in the Enlargement group than in the No Change group (39.3 vs 35.9 mm; P = 0.0058) (23.5 vs 18.2 mm; P = 0.000095). The principal component 1, which is the data calculated by elliptic Fourier analysis, was significantly lower in the Enlargement group than in the No Change group (0.020 vs - 0.072; P = 0.000049). The mean systolic blood pressure ≥130 mmHg, aortic diameter, false lumen diameter and principal component 1 were included in the Cox proportional hazard model as covariates to determine the significant predictive variable. Principal component 1 demonstrated the only significance with aortic enlargement on multivariate analysis (odds ratio = 0.32; P = 0.048). CONCLUSIONS: The analysed and calculated morphological data of the shape of the true lumen can be more effective predictive factors of aortic enlargement of type B dissection than the conventional factors.

Mouse spermatozoa with higher fertilization rates have thinner nuclei.

BACKGROUND: Although spermatozoa with normal morphology are assumed to have uniform fertilization ability, recent data show that even normal spermatozoa have considerable variation in their head shape which is associated with differences in fertilization ability. Appropriate quantitative indicators for good sperm morphology, however, remain unidentified. METHODS: Therefore, in an effort to identify such an indicator, we compared the nuclear contour of normal mouse spermatozoa by quantitative multivariate analysis using elliptic Fourier descriptors combined with principal component analysis. The spermatozoa were obtained from different strains and collection sites which have been shown to be associated with different fertilization abilities. RESULTS: We found that the head was 5.7% thinner in spermatozoa from the B6D2F1 (BDF1) strain, known to have a higher fertilization rate, than in those from the C57BL/6N (B6N) strain, which has a lower fertilization rate. Moreover, zona-penetrated spermatozoa in the perivitelline space consistently had 5.4% thinner heads than those isolated from the epididymis before ejaculation. The aspect ratio, which represents the sperm head thinness, uniquely distinguished these sperm populations, confirming its validity as a morphological indicator. DISCUSSION: Because aspect ratio has also been shown to characterize human spermatozoa, this unique morphometric indicator might be applicable to compare normal spermatozoa among multiple patients, which will greatly facilitate and enhance current reproductive technologies.

A complete survey of normal pores on a smooth shell ostracod (Crustacea): Landmark-based versus outline geometric morphometrics.

Pores and sensilla on ostracod shell have often been used in studies of ontogeny, taxonomy, and phylogeny of the group. However, an analysis of sexual dimorphism and variation between valves in the number and distribution of pores is lacking. Also, such studies have never been done on a widely distributed, morphologically variable, and weakly ornamented freshwater ostracod. Here, we survey pores in one such species, Physocypria kraepelini. We choose 27 homologous pores as landmarks for 2D-geometric morphometric analysis, with the aim to assess intersexual and between valves variation in size and shape relative to the Fourier outline analysis. This species has only simple (Type A) pores with and without a lip, and each pore carries an undivided sensory seta. Our results show that the total number of pores varies (from 270 to 296), but this is not associated with a specific valve. Males carry fewer pores than females, however no sex specific pores are found. Small intrapopulation divergence of the Cyt b molecular marker (1%) indicates that morphological variability is not species related. We found that P. kraepelini exhibits directional asymmetry of size and shape, sexual size dimorphism (SSD) but lacks sexual shape dimorphism (SShD). Two geometric morphometrics methods were congruent in the estimation of SSD, SShD, and directional asymmetry of shape but differ in the statistical evaluation of directional asymmetry of size. Contrary to other animal groups, our study suggests that ostracods have more pronounced directional asymmetry of shape compared to directional asymmetry of size.

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.