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opennotspecifiedFeb 2022View details →

Figure 3 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 3. Macrobiotus ariekammensis ariekammensis from Svalbard – buccal apparatus and the oral cavity armature seen in PCM: A, dorsoventral projection of the entire buccal apparatus; B, C, oral cavity armature visible from dorsal (B) and ventral (C) views, respectively; D, E, placoid morphology visible from dorsal (D) and ventral (E) views, respectively. Filled flat arrowheads indicate a single tooth in dorsal portion of the third band of teeth in the oral cavity, empty arrow indicates cuticular spike, empty indented arrowheads indicate central constrictions in first macroplacoids and faint subterminal constriction in second macroplacoid. Scale bars in µm.

opennotspecifiedFeb 2022View details →

Figure 2 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 2. Macrobiotus ariekammensis ariekammensis from Svalbard – claws: A, B, claws II and IV respectively, seen in PCM; C, single continuous cuticular bar and double muscle attachments on leg I seen in PCM; D, details of lunulae on leg IV seen in PCM. Empty flat arrowhead indicates discontinuous cuticular bar, filled flat arrowheads indicate double muscles attachments, filled indented arrowhead indicates cuticular bar. Scale bars in µm.

opennotspecifiedFeb 2022View details →

Figure 1 in The Macrobiotus ariekammensis species complex provides evidence for parallel evolution of claw elongation in macrobiotid tardigrades

Figure 1. Macrobiotus ariekammensis ariekammensis from Svalbard: A, habitus, dorsoventral projection (Hoyer's medium, PCM); B, cuticular pores on the dorsal part of the body seen in PCM; C, granulation on the external surface of leg III seen in PCM; D, granulation on the internal surface of leg III seen in PCM; E, granulation on the dorsal and dorsolateral surface of leg IV seen in PCM. Filled flat arrowhead indicates granulation patch on the external leg surface, empty flat arrowhead indicates the faint granulation patch on the internal leg surface, filled indented arrowhead indicates cuticular bar under claws, empty indented arrowhead indicates the cuticular bulge (pulvini). Scale bars in µm.

opencc-zeroOct 2022View details →

Mapping and assembly of the Midas cichlid male-specific region supports molecular parallelism in the evolution of a master sex-determining role for amhr2

The evolution of sex chromosomes and their differentiation from autosomes is a major event during genome evolution that happened many times in several lineages. The repeated evolution and lability of sex-determination mechanisms in fishes makes this a well-suited system to test for general and predictable patterns in evolution. According to current theory, differentiation is triggered by the suppression of recombination following the evolution of a new master-sex determining gene. However, the molecular mechanisms that establish recombination suppression are known from few examples, owing to the intrinsic difficulties of assembling sex determining regions (SDRs). Forward-genetics data and the development of long-read sequencing have generated a wealth of data questioning central aspects of the current theory. Here, we demonstrate that sex in Midas cichlids is determined by an XY system, identify and assemble the SDR by combining forward-genetics, long-read sequencing and optical mapping. We show how long-reads aid in the detection of artifacts in genotype-phenotype mapping that arise from incomplete genome assemblies. The male-specific region is restricted to a 100 kb segment on chromosome 4 that harbors transposable elements and a Y-specific duplicate of the anti-Mullerian receptor 2 locus, a known sex-determining gene. Our data suggests that amhr2Y originated by an interchromosomal translocation from chromosome 20 to 4 predating the split of Midas and Flier cichlids. In the later, it is pseudogenized and translocated to another chromosome. Duplication of anti-Mullerian genes is a common route to establishing new sex determiners, highlighting the role of molecular parallelism in the evolution of sex determination.

Fig. 11 in Parallel evolution of leaf morphology in gnetophytes

Fig. 11 Leaf venation patterns of Cretaceous gnetophytes. a Siphonospermum simplex Rydin et Friis. b–d Drewria potomacensis Crane et Upchurch (redrawn from Crane and Upchurch 1987)

Fig. 8 in Parallel evolution of leaf morphology in gnetophytes

Fig. 8 Reconstruction of Ephedra multinervia displaying dichasial branching pattern, the lengthy and strap-shaped leaves and the sessile two-seeded female cones having a receptacle. b bract, fru female reproductive unit, l leaf, r receptacle

Fig. 5 in Parallel evolution of leaf morphology in gnetophytes

Fig. 5 Nodal portion of a shoot of Ephedra multinervia. a The swollen node and the lengthy strap leaf. b The multiple dichotomizing parallel veins. c Connections of veins. l leaf, v vein, n node

Fig. 2 in Parallel evolution of leaf morphology in gnetophytes

Fig. 2 Leaf venation of the modern gnetophytes. a–b Ephedra (from Foster 1971). c Gnetum (from Rodin 1967). d Welwitschia (from Martens 1971)

Fig. 1 in Parallel evolution of leaf morphology in gnetophytes

Fig. 1 Phylogeny of the modern gnetophytes indicating the diversified morphology of leaves and female cones

opencc-zeroDec 2013View details →

Data from: Parallel evolution of jugal structures in Devonian athyridide brachiopods

Here, we describe Sinathyris crassa gen. et sp. nov., a new early Emsian (Early Devonian) athyridide brachiopod with a double spiralium from the Guangxi Province of southern China. Unlike the majority of genera of the subfamily Helenathyridinae, which possess accessory spiral lamellae developed directly from the jugal branches, the form described here shows these lamellae arising from a distally bifurcating jugal stem. These differences suggest that the double spiralium in S. crassa might have appeared independently from the double spiralium of the helenathyridins. To test the subfamily assignment of Sinathyris gen. nov., we carried out phylogenetic analyses, which indicate that the new genus is more appropriately referred to the Didymothyridinae. The cladistic analyses of the athyridides indicate that double spiralia have developed independently among these brachiopods at least five times during their evolutionary history.

opencc-zeroDec 2011View details →

Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.

opencc-zeroDec 2015View details →

Data from: Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution

Parallel divergence and speciation provide evidence for the role of divergent selection in generating biological diversity. Recent studies indicate that parallel phenotypic divergence may not have the same genetic basis in different geographical locations - "outlier loci" (loci potentially affected by divergent selection) are often not shared among parallel instances of phenotypic divergence. However, limited sharing may be due, in part, to technical issues if false positive outliers occur. Here, we test this idea in the marine snail Littorina saxatilis, which has evolved two partly isolated ecotypes (adapted to crab predation vs. wave action) in multiple locations independently. We argue that if the low extent of sharing observed in earlier studies in this system is due to sampling effects, we expect outliers not to show elevated FST when sequenced in new samples from the original locations, and also not to follow predictable geographical patterns of elevated FST. Following a hierarchical sampling design (within vs. between country), we applied capture sequencing, targeting outliers from earlier studies and control loci. We found that outliers again showed elevated levels of FST in their original location, suggesting they were not generated by sampling effects. Outliers were also likely to show increased FST in geographically close locations, which may be explained by higher levels of gene flow or shared ancestral genetic variation compared to more distant locations. However, in contrast to earlier findings, we also found some outlier types to show elevated FST in geographically distant locations. We discuss possible explanations for this unexpected result.

opencc-zeroNov 2019View details →

Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry

Color pattern mimicry in Heliconius butterflies is a classic case study of complex trait adaptation via selection on a few large effect genes. Association studies have linked color pattern variation to a handful of noncoding regions, yet the presumptive cis-regulatory elements (CREs) that control color patterning remain unknown. Here we combine chromatin assays, DNA sequence associations, and genome editing to functionally characterize 5 cis-regulatory elements of the color pattern gene optix. We were surprised to find that the cis-regulatory architecture of optix is characterized by pleiotropy and regulatory fragility, where deletion of individual cis-regulatory elements has broad effects on both color pattern and wing vein development. Remarkably, we found orthologous cis-regulatory elements associate with wing pattern convergence of distantly related comimics, suggesting that parallel coevolution of ancestral elements facilitated pattern mimicry. Our results support a model of color pattern evolution in Heliconius where changes to ancient, multifunctional cis-regulatory elements underlie adaptive radiation.

opencc-zeroAug 2021View details →

Parallel evolution of Varroa resistance in honey bees; a common mechanism across continents?

The near-globally distributed ecto-parasitic mite of the Apis mellifera honey bee, Varroa destructor, has formed a lethal association with Deformed wing virus, a once rare and benign RNA virus. In concert the two have killed millions of wild and managed colonies, particularly across the northern hemisphere, forcing the need for regular acaricide application to ensure colony survival. However, despite the short association (in evolutionary terms), A. mellifera populations across the globe have been surviving many years without any mite control methods. This long-term survival, or Varroa resistance, is consistently associated with the same suite of traits, recapping, brood removal and reduced mite reproduction, irrespective of location. Here we conduct an analysis of data extracted from 60 papers to illustrate how these traits connect together to explain decades of mite resistance data. For the first time we have potentially a unified understanding of natural Varroa resistance that will help the global industry achieve widespread miticide free beekeeping and indicate how different honey bee populations across four continents have resolved a recent threat using the same suite of behaviours.

Figure 7 in Parallel evolution of toepads in rock-dwelling lineages of a terrestrial gecko (Gekkota: Gekkonidae: Heteronotia binoei)

Figure 7. Micro-ornamentation on the terminal (FD) scales. Terrestrial lineages are displayed on the left (A, C), whereas saxicoline lineages are on the right (B, D). Magnification of each tile is shown in the lower left corner, with a scale bar in the lower right corner. A, fully developed setae of the terrestrial EA6 lineage with an average length of 14 µm (Supporting Information, Table S2). B, fully developed setae of the saxicoline CC lineage (av. length 28 µm, Supporting Information, Table S2). C, detail of the branched setae tips with spatulae of the terrestrial EA6 lineage. White arrows indicate branching points of a single seta. D, detail of the branched setae tips with spatulae of saxicoline Paluma-W lineage. White arrows again indicate branching points of a single seta, illustrating that setae of the saxicoline lineages branch more often. Note the different magnifications between C and D, and to a lesser extend between A and B.

Figure 5 in Parallel evolution of toepads in rock-dwelling lineages of a terrestrial gecko (Gekkota: Gekkonidae: Heteronotia binoei)

Figure 5. Ancestral state reconstruction of size-adjusted terminal scale width. Trait values (depicted by the colour scale) at the tips represent the mean size-adjusted scale widths for each lineage. Colour bars at each node represent 95% confidence intervals for the ancestral state reconstruction. Habitat use (ecology) is indicated by shape (EA6 is marked as both generalist and terrestrial, see Results). The reconstruction shows that the Paluma-W lineage and the clade containing CC, MI, and Paluma-E have independently evolved enlarged terminal subdigital scales. Note that the low relative scale width of MI (relative to the other saxicoline lineages), is mainly driven by their large SVL (see Fig. 4).

Figure 1 in Parallel evolution of toepads in rock-dwelling lineages of a terrestrial gecko (Gekkota: Gekkonidae: Heteronotia binoei)

Figure 1. Relationships and distributions of Heteronotia binoei lineages used in this study. A, maximum likelihood phylogeny of the relevant lineages inferred from ND2 sequences using RAxML, with bootstrap support values shown (see Supporting Information, Fig. S2 for the full H. binoei phylogeny). Circles denote terrestrial or generalist lineages, while triangles denote saxicoline lineages. Lineages without accompanying symbols are not displayed on the adjacent map (B), and the CQ lineage (*) was not included for morphological analysis. B, distributions of the focal lineages in north-eastern Queensland, with symbols and colours matching the adjacent phylogeny (A). C, an individual of the CC lineage on a granite boulder. D, subdigital view on the right hindfoot (pes) of the generalist EA6 lineage, and E, the saxicoline MI lineage.

Figure 2 in Parallel evolution of toepads in rock-dwelling lineages of a terrestrial gecko (Gekkota: Gekkonidae: Heteronotia binoei)

Figure 2. Examples of micro-ornamentation classifications used in this study. A, short, unbranched spinules with pointed tips on the mid-distal (MD) scales of EA6. B, flattened tips (indicated by black arrows) of the setae on the proximal-most MD scale (bordering the sub-inflection scale) of Paluma-W. C, spatulae (indicated by white arrows) on the tips of the setae on the terminal FD scale of Paluma-W. D, subdigital SEM image of an EA6 toe illustrating the different functional scale regions. The red line illustrates the measurement of terminal scale width.

Figure 4 in Mosaic patterns of homoplasy accompany the parallel evolution of suspensory adaptations in the forelimb of tree sloths (Folivora: Xenarthra)

Figure 4. Geometric morphometric principal components analysis of the ulna, humerus and scapula of xenarthrans. A, the first two axes of the ulna GM analysis. No other principal components (PC) axis accounts for more than 5% of variation. B, the first two axes of the humerus GM analysis. The small amount of variation accounted for by PC2 is likely due to the small sample sizes for the taxa it differentiates, specifically armadillos, the two giant ground sloths, and to a lesser extent Hapalops. PC3 accounts for 5.6% of variation and differentiates Cyclopes from Paramylodon and Glossotherium. No other axes account for more than 5% of variation. C, the first two PCs of the scapula GM analysis. PCs 3 and 4 account for 8.6% and 6.3% of variation, respectively. PC 3 separates Cyclopes from other taxa, and PC 4 separates Cyclopes and Dasypus from Choloepus. No other PC accounts for more than 5% of variation. Sloth scapula specimens identified with a thick rimmed circle and black dot indicate the specimens shown in 4D. D, Choloepus (centre) has a relatively conserved gross scapular morphology (compare with Paramylodon on right), especially when compared with Bradypus (left), but it has mapped functional traits such as an angled scapular spine onto that conserved bauplan. Squares indicate armadillos, rounded squares indicate anteaters, and circles indicate sloths.

Figure 5 in Mosaic patterns of homoplasy accompany the parallel evolution of suspensory adaptations in the forelimb of tree sloths (Folivora: Xenarthra)

Figure 5. Geometric morphometric phylomorphospace of the ulna, humerus and scapula. A, phylomorphospace of the ulna shows that tree sloths inhabit the same region of morphospace, suggesting extensive parallel evolution relative to their last common ancestor, while giant ground sloths and armadillos diverged in the opposite direction and anteaters appear to have diverged little from the last