Category Archives: Evolution

INTRODUCTION

Whole-genome duplication (WGD) or polyploidy provides genomic opportunities for evolutionary innovations and adaptation (14). Polyploidy is rare in animals, possibly because of barriers to sex determination, and physiological and developmental constraints, especially nuclear-cytoplasmic interactions and related factors (5, 6). Further, polyploid animals appear to be incapable of coping with genomic and developmental chaos resulting from the merging of two genomes because of changes in structural variation, regulatory imbalance, gene expression bias, and activation of transposable elements (TEs), as documented in many other allopolyploids (1, 3, 710). A newly formed allopolyploid line of fishes (11) experienced more severe chaotic changes than polyploid plants (7, 8, 10, 12, 13). These rapid and dynamic changes have genetic and epigenetic bases (7, 14). Biased subgenomic changes may help alleviate chaos from genome mergers (15), and subsequent coordination may help stabilize the subgenomic functions in newly synthesized allotetraploid plants (7, 12, 16) after the initial genome shock (17) between divergent subgenomes that coexist in the same cell nucleus. However, the long-term consequences for polyploid animals in rediploidization remain elusive.

Goldfish (Carassius auratus red var.) belongs to family Cyprinidae in the most specious order of fishes (Cypriniformes), which contains many polyploid species (1820). The tetraploid carp was domesticated hundreds of years ago in China and Europe, and it is the economically most important fish in freshwater aquaculture (21). Goldfish (C. auratus red var.) is the most commonly kept pet globally, and it constitutes a model system for studying neurobiology and physiology. This allotetraploid (2n = 4x = 100) species was formed by the interspecific hybridization of two diploids (2n = 2x = 50); subsequent chromosome-doubling restored meiotic paring and disomic inheritance (18, 19). Goldfish has nearly twice as many chromosomes as zebrafish and most of other cyprinids (22, 23). Its numerous small chromosomes pose a great challenge to assembling and annotating both subgenomes at the chromosomal level. Because no extant diploid progenitors are available for study, the evolution of this complex polyploid genome remains poorly understood (21, 24, 25), despite the recently published draft genome (26).

Here, we report a reference-quality, chromosome-scale assembly of goldfish including identification of both subgenomes and analysis of the variation and expression changes between them. We also evaluate the subgenomic evolution of goldfish and common carp. Our results indicate that allotetraploid goldfish and common carp have diverse strategies for balancing dynamic subgenomic diversification during continuous rediploidization. The diverse and continuous evolutionary processes broaden our understanding of the evolution and function of genomes in allopolyploid vertebrates and may explain why most polyploid animals fail to survive.

Allopolyploid genomes are much more complicated than diploid ones due to their polynomic inheritance and gradual random decay of progenitors genomes during rediploidization (2, 3). A high-quality genome assembly is required to discriminate changes from related species in allopolyploids. Our high-quality genome of a gynogenetic goldfish (C. auratus red var., n = 100) was assembled using data from a combination of three technologies (Fig. 1), including 325.34 gigabases (Gb; 203) of Illumina sequence data (Illumina GAII, HiSeq 2000), 128.51 Gb (80) of single-molecule real-time (SMRT) long reads (PacBio RS II and Sequel), and 231.50 Gb of clean BioNano mapping data (Bionano Genomics Irys). The final assembly consisted of 5477 scaffolds, with a scaffold N50 of 2.94 megabases (Mb) after gap filling (Table 1 and data S1_14), which resulted in a genome size of 1.64 Gb. This was similar to the size estimated by flow cytometry (1.71 Gb; Fig. 1) and slightly higher than the k-mer analysis (1.43 Gb; Fig. 1). In addition, using 307.46 Gb of data generated by high-throughput chromosome conformation capture sequencing (Hi-C seq) technology (Annoroad Gene Technology Co. Ltd., Beijing; data S1_5, 6), 1.59-Gb (96.95%) genome-level sequences were aligned and ordered into 50 scaffolds that potentially matched the chromosomes (Table 1, fig. S1A, and data S2_1). A genetic map consisting of 50 linkage groups was constructed in 79 F2 offspring using 7466 single-nucleotide polymorphism markers developed from 147.10 Gb of RNA sequencing (RNA-seq) data (27). Next, the genome scaffolds (1.07 Gb, 65.24%) were anchored on the genetic map (data S2_2). Sequence assemblies on the pseudochromosomes matched perfectly to the anchored 50 linkage groups, confirming the high-quality assembly of the allotetraploid goldfish genome (fig. S1, B and C, and data S2_35). BUSCO and CEGMA showed the assemblies to be complete (data S2_6). Our assembly conformed to Vertebrate Genome Project standards for reference genomes (https://vertebrategenomesproject.org/) and covered more sequences than the published goldfish genome by Chen et al. (26), which consisted of 1.24 Gb with an anchor ratio of ~66% from 1.82 Gb contigs (Table 1). Subsequently, we compared the completeness and collinearity between our assembly and the published genome using MUMmer (v3.23), based on the minimum clustering unit of 50 kilobases (kb), which is the smallest unit that we could check, and consistent with 50-kb resolution of Hi-C clustering. Within the total length of 1.06-Gb collinearities from 2380 clustering groups, we found general consistency, while some structural differences existed between the two. In our study, among 277 inversions and 1338 translocations identified, 63.95% were validated by PacBio long reads, optical map, and/or Hi-C data (Fig. 2A, fig.S1D, and data S2_7, 8). These efforts obtained a general improvement of quality scores in our genome assembly relative to the published data. For example, the optical map and Hi-C analyses obtained improvement at an inversion boundary (Fig. 2A).

(A) Genome size and karyotype of goldfish. (a) Image of a gynogenetic goldfish (C. auratus var.). Photo credit: Shaojun Liu, Hunan Normal University, China. (b) Diagram of C value. The X axis presents the fluorescence index, and the Y axis presents the frequency of cells. Sample/calibration ratio equals the peak X value of the calibration sample divided by X value at the peak of the target sample. The first sharp peak with green dashed line displays the X axis and cell frequency of chicken blood, and the second one with red dashed line represents the X axis and cell frequencies of goldfish. C value of sample is sample/calibration ratio calibration samples C value. (c) Goldfish have 100 chromosomes and 100 signals after the chromosomes are stained with DNA probe (probe A) [9468-bp fragment of 36 copies of a repetitive 263-bp fragment; adopted from Liu et al. (11)]. (B) Sequencing technologies for primary assembly. (C) Genome assembly, Hi-C cluster, and genetic map construction. Genome size assessment by k-mer analysis is performed by 40 Illumina paired-end reads after the primary assembly. Next, scaffolds are clustered into 50 pseudochromosomes by using Hi-C data obtained by chromosomes; the genetic map was constructed by using the data of Kuang et al. (27) (D) Annotation and chromosome-scale organization. Annotation of scaffolds was performed using a combination of ab initio prediction, transcript evidence gathered from RNA-seq of embryos and eight kinds of adult tissues (gonads, brain, liver, spleen, kidney, eye, epithelium, and fin), and homologous genes information from five fish genomes, by using EVidence Modeler (EVM). Final set of 50 pseudochromosomes was generated after pairwise validation among Hi-C clustering results, genetic map, and collinearity analyses. (E) Subgenome identification. After extracting the homologous genes of goldfish and other species, the species tree is constructed by using single-copy genes from 10 genomes. Gene trees were constructed by defining homologous gene clusters using whole-genome sequences/transcripts from 10 cyprinid species of Cyprininae (C. auratus, Cyprinus carpio), Labeoninae (Labeo rohita), Poropuntiinae (Poropuntius huangchuchieni), Schizothoracinae (Schizothorax oconnori, Schizothorax waltoni, Schizothorax macropogon, and Schizothorax kozlovi), Danio rerio, and Ctenopharyngodon idellus. After comparing the species tree and nucleic gene trees, the matrilineal (clustered with Schizothorax) and patrilineal markers from the gene trees were labeled back to 25 pairs of pseudochromosomes. The origin of pseudo-chromosomes was identified by most of the supported markers.

NGS, next-generation sequencing; LG, linkage group.

(A) Diagrams displaying the rearrangement identified in the syntenic blocks between our assembly and the goldfish genome published by Chen et al. (26). The syntenic block between two assemblies was identified with an inversion event (a), in which the rearranged boundary on our genome was continuously covered by the long reads of the optical map (b), and supported by the strong clustering signal from the heat map (c) constructed by high-depth sequencing data from chromosome conformation capture technology. (B) Allotetraploid goldfish and common carp genome synteny. Blocks represent the genomic overview of assembled chromosomes of subgenome M and subgenome P from goldfish and subgenome B and subgenome A from common carp (Hebao red carp) (29). Colored lines indicate the orthologous sites of gene blocks and their colinear relationships between subgenomes M and B and subgenomes P and A, respectively. Numbers M01 to M25, P01 to P25, B01 to B25, and A01 to A25 indicate the homologous chromosomes of M and P subgenomes from goldfish, and B and A subgenomes from common carp, respectively, numbering in order according to the collinearity relationships to zebrafish genome (fig. S3). The numbers beside M and P chromosomes indicate the supporting rate from homoeologous gene makers with clear origin of parental ancestor determined by the gene trees. (C) Phylogenetic relationships and timing of WGD/polyploidization events in Cyprininae, with nodes based on protein-coding genes of goldfish, common carp, golden-line barbel, grass carp, and zebrafish. Dated divergence time of grass carp and the ancestor of Cyprininae was 20.9 Ma ago, and the putative matrilineal and patrilineal progenitors were 15.1 Ma ago (T1), after the WGD event (T2). Divergence of the polyploid Cyprininae radiation was dated at 13.8 Ma ago (T3), and the divergence between goldfish and common carp was dated at 10.0 Ma ago (T4). Orange and blue branches indicate the putative M and P progenitors, respectively. Photo credit: Goldfish and common carp by Shaojun Liu, Hunan Normal University, China; golden-line barbel and grass carp from FishBase; zebrafish from Wikimedia. (D) Phylogenetic tree based on protein-coding genes from single-copy orthologs, rooted with human and chicken. Alignments were performed by MUSCLE, and the maximum likelihood tree was reconstructed by PhyML.

The annotation predicted 43,144 genes with an average length of 17,025 base pairs (bp) and 9.78 exons per gene (data S1_7 and data S2_9). Of the genes, 39,205 (90.87%) were functionally annotated (data S2_9). Accuracy and completeness of the annotation were validated further through 97.78% coverage of annotated genes by RNA-seq data. The annotation included 6788 transfer RNA (tRNA), 1380 ribosomal RNA (rRNA), 1324 small nuclear RNA (snRNA), and 3385 microRNA genes (data S2_10). Repeat annotation indicated an overall repeat content of 39.49% (data S2_11), which was less than the 52.2% of zebrafish (28) and comparable to ~40% of African clawed frog (9). The most abundant TEs in the goldfish genome were type II, which represented 21.19% of the whole-genome sequence. Other annotated TEs included 174 superfamilies.

To identify the goldfishs subgenomes from two progenitors, we used phylogenetic information of the Cyprininae (18, 19). Several species in the genera Carassius (including goldfish) and Cyprinus were reported to have undergone the same allopolyploidization approximately 10 to 12 million years (Ma) ago (19). The matrilineal copy of several nuclear genes was grouped with genus Schizothorax (18, 19), and they diverged from the patrilineal ones 17 to 19 Ma ago (18, 19). By comparing phylogenies between the mitogenomes and homoeologous gene pairs of whole-genome sequences/transcripts from 10 cyprinid species, analyses confirmed that Schizothorax was monophyletic; it shared a matrilineal ancestor with all allotetraploid species of Cyprininae (Fig. 1E and data S1_8). The analysis identified 1274 homoeologous gene pairs of goldfish. Mapping these homoeologous gene pairs onto the 50 pseudochromosomes identified matrilineal (M) and patrilineal (P) subgenomes, with an average support rate of 95.34% (Fig. 2B and table S1). To clarify the relationship between each subgenome pair of goldfish and common carp (Hebao red carp) with subgenomes of A and B of Xu et al. (29), we first constructed the collinearity relationship between the two species. Analyses using MCScanX found that 9266 orthologous gene pairs had unambiguous one-to-one relationships between subgenome M (from goldfish) and subgenome B (from common carp), and 6991 orthologous gene pairs had clear one-to-one relationships between subgenome P (from goldfish) and subgenome A (from common carp; Fig. 2B). The results showed a consistency of 74.58% between subgenomes M and B and 66.97% between the subgenomes P and A. This suggests that subgenomes M and B are from the matrilineal genome of the Cyprininae ancestor, while subgenomes P and A are patrilineal ones (Fig. 2B and data S2_12, 13).

The ancient WGD within Cyprininae was identified via phylogenetic analyses of genome-wide markers, which integrated subgenomes M and P. Analyses compared both subgenomes of goldfish, common carp, and golden-line barbel (Sinocyclocheilus grahami) to zebrafish and grass carp. A MCMCTree analysis in the Phylogenetic Analysis by Maximum Likelihood (PAML) package (v4.8) (30) with four calibration points suggested that the progenitor-like genomes diverged approximately 15.09 Ma ago (T1; Fig. 2C). Following allopolyploidization (T2), S. grahami originated about ~11 Ma ago (T3), followed by goldfish and common carp at ~9 Ma ago (T4). These dates were more recent than those (13.75 and 9.95 Ma ago, respectively) estimated by using 568 single-copy genes (Fig. 2, C and D, and fig. S1E). The new estimate (13.75 to 15.09 Ma) of timing for the Cyprininae WGD (T2; Fig. 2C) was earlier than those (10 to 12 Ma ago) based on gene markers (19). The expansion and contraction of gene families were estimated to infer the evolutionary history after the Cyprininae-specific WGD event relative to the teleost-specific WGD event in zebrafish and grass carp (fig. S1, F and G, and data S2_14). Within 4453 expanded gene families, there were 313 transcription factors, indicating a significant abundance (P < 0.01, Fishers exact test). Most of them were known to be involved in embryonic development, especially organogenesis during differentiation of germinal layers (fig. S1H).

Evolution of subgenomes has been reported in allopolyploid angiosperms (8, 10) and vertebrates (9). They typically showed conservation of one progenitor-like genome and diversification of the other by large structural variation in collinearities compared to the ancestral genome. In contrast, comparison of allotetraploid goldfish annotated genes, repeats, and noncoding RNAs (ncRNAs) showed approximately equal representations between the two subgenomes. Approximately 1.5 Gb of chromosome-scale sequences were partitioned into subgenomes M and P, which was consistent with the number of genes in M (20,913, 52.07%) and P (19,248, 47.83%). The proportions of repeat sequences and ncRNAs were also similar between the two subgenomes (data S3_1). Thus, the two subgenomes had similar gene densities and distributions in most chromosomes, except for significantly higher densities in three M (chr1, chr20, and chr43) and one P (chr27) chromosomes (P < 0.05, two-tailed paired t test; data S3_2). The two subgenomes also contributed similar proportions of all TE families with annotation against public database (fig. S2, A and B, and data S3_3). Further, the comparison between two subgenomes of common carp in genomic contents showed nearly equal representations between subgenomes B and A (29).

To further investigate the evolution of two subgenomes after allopolyploidization in carp-like fishes, we compared subgenomes M and P of goldfish and subgenomes B and A of common carp with zebrafish to define the changes in synteny and genomic divergence. To integrate the collinearities between goldfish and common carp, we aligned 43,144 high-confidence gene models to 50 goldfish and the 25 zebrafish chromosomes. The results indicated that 12,450 genes of subgenome M and 11,042 genes of subgenome P were located on syntenic blocks (P = 1.09 105), and 7568 orthologous gene pairs had a clear two-to-one relationships to zebrafish (Fig. 3A and fig. S3). Collinearities between homologous goldfish M and common carp B chromosomes identified 15.12% inversions and 10.30% translocations, and the ones between goldfish P and common carp A chromosomes showed 22.29% inversions and 10.74% translocations, which indicated more rearrangement in the patrilineal subgenomes (data S2_12). We also validated the boundaries of all rearranged regions identified by both collinearities against goldfish from Chen et al. (26) and common carp; 69.01% of regions on subgenome M and 67.64% on subgenome P were assembled continuously in our genome by sequencing data (data S3_4). With respect to GC (guanine-cytosine) content and repeat densities, we used a sliding window of 50 kb for comparative analysis. We found that the patrilineal subgenomes P and A had greater GC content than matrilineal subgenomes M and B (Fig. 3B, a, and data S3_5), indicating subgenome-specific variation in these two species. However, the distributions of repeat densities yielded an opposite pattern; more repeats occurred in subgenome P than M in the goldfish, and in the common carp, more repeats were in B than in A. These differences may have owed to species divergence (Fig. 3B, b, and data S3_5). The distributions of GC content and repeat density might contribute to different kinds of divergence (data S3_5). In addition, we obtained 28 and 16 specific blocks with significantly biased repeat densities between subgenomes in goldfish and common carp, respectively, and labeled those potential sources of divergence between the two species on each chromosome (P < 0.05, Wilcoxon rank sum test; Fig. 3A, fig. S3, and data S3_6).

(A) Syntenic blocks between goldfish and common carp and syntenic blocks between goldfish and zebrafish with color-labeled rearrangements in two examples. The other 23 groups of syntenic analysis are shown in fig. S3. All 50 pseudochromosomes of goldfish show clear two-to-one orthologous relationships to the 25 chromosomes of zebrafish. Orange bars and numbers mark the chromosomes from matrilineal (M and B) subgenomes, while blue denotes the patrilineal (P and A) ones. Gray bars and numbers mark the chromosomes of zebrafish. Light gray lines indicate the syntenic blocks, light orange lines indicate the rearrangements between goldfish and common carp, and the pink lines indicate the rearrangements between goldfish and zebrafish. The red and black bars on each chromosome indicate the biased repeat densities, in which the red ones indicate the syntenies with significantly higher repeat densities relative to the black ones (P < 0.05, Wilcoxon rank sum test). (B) Boxplots of distributions of (a) GC content and (b) repeat density in consistent syntenies, rearranged regions, and the boundaries of rearranged regions. Orange and blue boxes mark the values from matrilineal (M and B) and patrilineal (P and A) subgenomes, respectively. Boxes with black lines indicate the distributions of goldfish, and the ones with dashed lines indicate the common carp. (C) Distributions of consecutive gene retentions in subgenomes M and P, which do not differ from each other significantly (Fishers exact test, P = 0.35). (D) Dating the time of pseudogene formation in subgenomes M and P of goldfish, subgenomes B and A of common carp, as described in Supplementary Methods and Analysis 6. X axis represents an estimated time of pseudogene formation; Y axis represents the frequencies of pseudogenes in every 0.5-Ma unit. Orange lines display the frequencies of pseudogenes on subgenomes M or B along time (X axis), and blue lines display the frequencies of pseudogenes on subgenomes P or A. Gray bars indicate the timing of allopolyploidization (13.8 to 15.1 Ma ago). (a) and (b) display the distributions of all pseudogenes frequencies from each subgenome along time in goldfish and common carp; (c) and (d) display pseudogenization events specific to each subgenome in goldfish and common carp. (E) Boxplot displays the distributions of Ka/Ks ratios for (a) 7568 homoeologous gene pairs between M and P subgenomes calculated against zebrafish and grass carp and (b) distributions of Ka/Ks ratios displayed in boxplot for (a) 7568 homoeologous gene pairs between subgenomes B and A calculated against zebrafish and grass carp. Central line in each boxplot indicates the median value. Top and bottom edges of the box indicate the 25th and 75th percentiles, and the dashed lines extend 1.5 times the interquartile range beyond the edges of the box.

Most genes (>88%) were retained in both subgenomes, and the distribution of consecutive (more than two contiguous genes) retentions of syntenic blocks was not biased between them (P > 0.05; Fig. 3C and fig. S2C). The tracing of the gene loss by deletion showed 1737/2727/1677 M/P/shared losses in goldfish and indicated that subgenome P experienced more small-scale deletions of genes (11.53% of 23,652) than subgenome M (7.14% of 24,327; P < 0.01). In common carp, 1009/1409/1574 B/A/shared losses indicated more small-scale deletions in subgenome A (6.98% of 20,172) than B (4.81% of 20,977). Subgenome P tended to lose more genes related to pathways of amino acid metabolism, oxidative phosphorylation, base repair, and homologous recombination (fig. S2C and data S4_1) than subgenome M. Genes lost across all subgenomes occurred in no more than two consecutive genes in all syntenic blocks of zebrafish (data S3_7). Analyses identified fewer pseudogenes in subgenome M (2.90%, 705/24,327) than P (4.33%, 1023/23,652; P < 0.01) and also fewer pseudogenes in B (2.33%, 486/20,815) than A (3.86%, 754/19,509).

According to the dating of pseudogene formation, pseudogenes accumulated continuously in both goldfish and common carp (Fig. 3D). In goldfish, pseudogenes formed asymmetrically and continuously after allotetraploidization, while in common carp, both subgenomes experienced the accelerated accumulation of pseudogenes after allotetraploidization (Fig. 3D, a and b). To test whether the functional loss continued after the divergence between the two species, we grouped the pseudogenization events into the one shared by two species, either MB or PA, and the other occurred specifically in each subgenome. Subgenomes M and B shared 79 pseudogenes, while P and A shared 156. These shared pseudogenes in the patrilineal subgenomes of goldfish and common carp were involved in pathways of base excision repair and homologous recombination (data S4_2). We found 626/867/407/598 pseudogenes specific to M/P/B/A subgenomes, respectively, which suggested that more gene loss events occurred independently in each subgenome than the ones they shared. The dating of pseudogenes specific to each subgenome showed the same distributions after the divergence of both species: continuous accumulations in goldfish (Fig. 3D, c) and accelerated accumulation of pseudogenes in common carp (Fig. 3D, d). Notably, the pseudogenes specific to subgenome P were also predicted to be involved in DNA repair and homologous recombination (data S4_3). Together, these analyses supported a bias in gene loss between goldfish and common carp.

Nonsynonymous mutation (Ka) values, synonymous mutations (Ks) values, and the ratios of these values (Ka/Ks) between the two subgenomes were compared against the reference genomes of zebrafish and grass carp to identify alterations in evolutionary rates. In goldfish, all homoeologs in subgenome M (zebrafish median Ka/Ks = 0.12; grass carp = 0.18) had a significantly lower Ka/Ks ratio than those in subgenome P (median Ka/Ks = 0.13 and 0.19; P < 0.01 for both, Wilcoxon rank sum test; Fig. 3E), while single-copy genes and all genes showed no significant bias between the two subgenomes (P > 0.05; data S3_8, 9). In common carp, both homoeologous and all genes in subgenome B had significantly lower Ka/Ks ratio than in subgenome A (P < 0.01), while single-copy genes showed no significant bias between the two subgenomes (P > 0.05; data S3_8, 9). Ka and Ks values and Ka/Ks ratios in syntenic blocks indicated that no significant correlation existed with structural changes (fig. S2, D to F). The distributions of Ka/Ks ratios between each paired M and P, or paired B and A, chromosomes also showed no difference (fig. S2G); only three syntenic blocks showed a significant biased Ka/Ks ratio between subgenomes M and P, while only seven syntenic blocks were biased significantly between subgenomes B and A (P < 0.05, Wilcoxon rank sum test). These results indicated species-specific gene fates. Signatures for positive selection occurred in 128 homoeologous genes in goldfish, symmetrically including 0.31% (65/20,913) of genes in M and 0.33% (63/19,248) in P. Statistical comparisons of both overall and pairwise homoeologous chromosomes detected significant differences between matrilineal and patrilineal subgenomes, as well as species-specific changes.

More species-specific alterations occurred between parental genomes than asymmetrical changes. This might had led to the diversities of expression in homoeologous gene pairs. To test for this, we compared transcriptome changes between the subgenomes in six adult tissues and 15 developmental stages using the homoeologous genes that were confirmed with high correlations between biological duplicates and among developmental stages (fig. S4, data S1_9, and data S3_10, 11). In goldfish, expressions of homoeologous gene pairs did not show a bias between the homoeologs among all six adult tissues or at eight developmental stages. This pattern held except in seven specific stages around the reprogramming of embryogenesis (31, 32), where M subgenomic homoeologs were expressed 4.8% higher than the P ones (Fig. 4, A and B). In common carp, expression of homoeologous gene pairs showed B-biased expression in five stages around the reprogramming of embryogenesis, one stage in pharyngula period, and two stages in hatching period (Fig. 4C).

(A) Boxplot of log10(TPMM/TPMP) for homoeologous gene pairs showing medians in six adult tissues of goldfish. Red dashed line shows the equal ratio of log10(1). All adult tissues show no bias of expression between genes stemming from the subgenome M or P. (B) Boxplot of log10 [(TPMM + 0.1)/(TPMP + 0.1)] for homoeologous gene pairs showing medians in 15 developmental stages of goldfish [16 cell, 32 cell, 64 cell, 128 cell, 1000 cell; 8, 12, 16, 18, 24, 30, 46, 64, 71, and 84 hours post-fertilization (hpf)]. Red dash shows the equal ratio of log10(1). Time points from 64-cell to 22-somite stages biased expression of M homoeologs, which average 4.8% more than P genes within homoeologous gene pairs; early embryos (16- and 32-cell stages), pharyngula, and hatching period embryos show no bias of expression. (C) Boxplot of log10 [(TPMB + 0.1)/(TPMA + 0.1)] for homoeologous gene pairs from common carp shows medians in zygotically controlled developmental time points. Red dashed line shows equal ratios of log10(1). Time points from 32-cell to germ ring, 25% otic vesicle closure (OVC), long pec, and pec fin stages indicate biased B-homoeolog expression; other stages show no expression bias. (D) Expression patterns of 9090 homoeologous gene pairs from goldfish where the trend displays expression of either biased toward M or P homoeologs (EBM or EBP; 6223 genes in total, 68.46%) when gene pairs are coexpressed in at least one development stage. (E) Expression trend of 9090 homoeologous gene pairs from goldfish displaying an expression shift between two homoeologs (ES; 1644 genes in total, 18.09%) where one copy is expressed higher than the other at earlier time points, then the other copy surpasses it in later development stages. (F) Expression patterns of 4241 homoeologous gene pairs from common carp where the pattern displays either biased B- or A-homoeolog expression (2811 gene in total, 66.28%) when homoeologous gene pairs coexpressed in at least one development stage. (G) Expression patterns of 4241 homoeologous gene pairs that indicate expressional shift between two homoeologous gene pairs (414 gene in total, 9.76%); one homoeologous gene copy expressed higher than the other at an earlier time point, then the other copy surpasses it later in development. Patterns include two groups: genes (185, 4.36%) with ES before germ ring stage and genes (229, 5.40%) with ES post-germ ring stage, which accounts for most genes. Among the ES genes, 32 (0.75%) have more than two time shifts. (H) Comparison of DNA methylation levels between the two subgenomes in brain and liver tissues. (I) Comparison of DNA methylation levels between the two subgenomes in embryos of 12 developmental stages.

In goldfish, the number of differentially expressed homoeologs differed among developmental stages (fig. S5), and their expression levels exhibited spatial and temporal variation throughout development. Expression of 9090 homoeologous gene pairs showed three patterns. First, most gene pairs (68.46%, 6223/9090) displayed an expression bias toward either M (39.69%, 3608) or P (28.77%, 2615) homoeologs (Fig. 4D and Table 2). Second, expression shifted between two homoeologs (18.09%, 1644/9090) during different developmental stages (Fig. 4E and Table 2). Among them, 11.88% (1080) displayed a shift after the reprogramming of embryogenesis, while 184 genes shifted more than once through various developmental stages. Third, 13.45% of homoeologs (1223/9090) were expressed equally throughout all developmental stages. Approximately 39.69% homoeologous pairs displayed biased expression toward the M homoeologs throughout all development stages with a slightly higher expression levels in stages around germ ring, while 18.09% homoeologous gene pairs were equally expressed. These trends were consistent with those in the common carp using the same analysis with 4241 homoeologous pairs (Fig. 4, F and G, and Table 2). The expression-bias shift of both M/B and P/A genes occurred most frequently in the germ ring of the gastrula stage, which is crucial for germ-layer development in both goldfish (395 shifts) and common carp (117 shifts; data S3_12).

EBM, expression bias toward matrilineal (M and B) homoeologs; EBP, expression bias toward patrilineal (P and A) homoeologs; ES, expression shift between two homoeologs.

In goldfish, Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses found overrepresentation of the M- and P-preferentially expressed genes of goldfish in 91 pathways (data S4_4, 5) and of expression-bias shifted genes in 61 pathways (data S4_6). Most of these preferentially expressed homoeologs shared enrichment of 13 pathways, while some M- and P-preferred genes were overrepresented in DNA replication and repair and in spliceosome and phototransduction, respectively. The results indicated that homoeologous genes from both subgenomes contributed similarly to biological pathways (fig. S6, A to D).

DNA methylation could have occurred during polyploidization, and the methylation-associated genes could have been inherited as epialleles (33). In goldfish, the subgenomes had indistinguishable levels of DNA methylation (difference less than 20%) in both gene body and promotor regions (fig. S7) in brain and liver tissues and among 12 developmental stages (Fig. 4, H and I, and data S1_10). A high level of DNA methylation in early stages of embryos was inherited from the sperm rather than eggs and decreased over time during development (fig. S7, A and B). Expression levels of homoeologous gene pairs correlated negatively with DNA methylation patterns, especially in the proximal promotor regions (figs. S7, C and D, and S8). Thus, DNA methylation may have played a role in the regulation of homoeologous gene expression. Analyses of co-DNA methylation by weighted gene coexpression network analyses (WGCNA) (34) identified 182 homoeologs (12.5%, 182/1454), with the DNA methylationlevel shifts between M and P homoeologs corresponding to their expression shifts but with no significant difference in either promoter or gene body regions among embryos of 12 time points (P > 0.05, Fishers exact test; fig. S7, E and F, and data S3_13).

Polyploid vertebrates such as goldfish and common carp might have experienced chaotic changes in their early stages of polyploidization (15 Ma ago), as reported in newly formed allopolyploid fishes (11) and in other newly synthesized polyploid plants (7, 12, 13). Our analyses of goldfish and common carp indicate similarities and differences in structural change. Significant bias (P < 0.05, Wilcoxon rank sum test) occurs in Ka/Ks ratios in homoeologous gene pairs between subgenomes M and P in the goldfish (M < P), and yet no significant bias occurs in Ka/Ks in single-copy genes. This suggests that the goldfish genome was prone to retain functionally constrained genes after its WGD (35). Specifically, the goldfish genome usually retains only one copy of homologous DNA repairrelated genes, which is consistent with the pattern in plants (36). Further, goldfish subgenome P continues to lose these genes via pseudogenization, yet this does not occur in common carp subgenome A, suggesting variable strategies in different species. This provides functional flexibility for both subgenomes during evolution and adaptation. Likewise, biases in post-polyploidization gene loss have been studied in plants (37, 38), and more work is necessary to elucidate this both in plants and animals. Our analyses reveal that short fragment loss only involved one or two consecutive genes of subgenomes M and P; this differs from flowering plants and African clawed frog, which have lost more and longer fragments (9, 10, 38). Considering gene expression, a few surviving animals could have evolved a balanced strategy to maintain genome stability. This would limit structural changes and genomic diversification by reprogramming homoeologous gene expression during embryonic development, which is critical for survival in both natural and controlled environments. Cyprinines can serve as models for investigating the evolution of vertebrate polyploidization, and they may explain why polyploidization events are far less common in animals than in plants. The dosage balance hypothesis is an attractive explanation for the patterns of post-polyploidization gene retention and loss (39), and future functional work is necessary to completely paint the picture.

Three gynogenetic goldfish from the same inbred line were collected to extract genomic DNA (data S1). DNA from one fish was used in whole-genome sequencing by Illumina and SMRT (Pacific Biosciences) sequencing platforms. We used wtdbg (v1.1.006) (40) to assemble the long reads and polished the resulting contigs with short reads. Another goldfish was sampled for optical mapping (BioNano Genomics Irys) and Hi-C library construction, which produced chromosome-level scaffolds. For the RNA-seq, eight adult tissues were sampled from one male and one female goldfish. Two groups of mature eggs and embryos were taken from 15 developmental stages of goldfish [16 cell, 32 cell, 64 cell, 128 cell, 1000 cell, 8 hours post-fertilization (hpf), 12 hpf, 16 hpf, 18 hpf, 24 hpf, 30 hpf, 46 hpf, 64 hpf, 71 hpf, and 84 hpf] and 14 developmental stages of common carp for RNA-seq. Further, brain and liver tissues and embryos from 12 developmental stages of goldfish were sampled for whole-genome bisulfite sequencing (WGBS). All experiments were approved by Animal Care Committee of Hunan Normal University (2014278) and followed guidelines of the Administration of Affairs Concerning Experimental Animals of China.

On the basis of the scaffolds linked by the Irys optical map, 50 pseudochromosomes were clustered with the Hi-C data. Next, a genetic map of goldfish based on genotyping was constructed by adopting the pooling-sequenced transcriptomic data of Kuang et al. (27), which were based on an inbred line of two parents and 79 F2 individuals. Subsequently, the two-to-one colinear relationships between goldfish and zebrafish were identified by using MCScanX (41). Last, 25 homologous chromosome pairs were generated after pairwise validation among Hi-C clustering results, genetic map, and collinearity analyses.

Protein-coding genes were annotated using a combination of ab initio prediction, transcript evidence gathered from RNA-seq of embryos and 16 adult tissues (ovary/testis, brain, liver, spleen, kidney, eye, epithelium, and fin for both female and male), and homologous genes prediction from five fish genomes (Ctenopharyngoden idellus, Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridi, and Sinocyclocheilus anshuiensis), with EVidence Modeler (v1.1.1). Functional annotations mainly included the following methods: (i) searching against known sequence data (Swiss-Prot/Gene Ontology) by BLASTP with E value at 1 105 and online comparison against the KEGG database by KEGG Automatic Annotation Server (KAAS) and (ii) InterProScan (v5.21-60.0) predicted conservative motifs and domains.

OrthoMCL (42) was used to cluster gene families for zebrafish, grass carp, golden-line barbel, common carp, goldfish, and species of Schizothorax. PhyML (v3.1) (43) was then used to build the phylogenetic trees for each gene family. A species tree was also constructed by using single-copy genes from the above 10 genomes. In the topology of gene trees, homoeologs located in the same clade with Schizothorax were considered to be M markers, while the remaining P copies constituted the hypothetical P species. The M/P markers were labeled back to 25 pairs of pseudochromosomes. The origins of pseudochromosomes were thereby identified by most of the M/P markers.

Times of speciation and progenitors divergence were estimated by the divergence time using MCMCTree in the PAML package (v4.8) (30). The general time reversible (GTR) nucleotide substitution model was used with a relaxed clock analysis. The multiple calibration points based on literature and fossil records were listed in detail in Supplementary Methods and Analysis 5. We used the divergence time of putative M and P progenitors in Cyprininae, and synonymous substitution levels between putative maternal and paternal homoeologs in goldfish, common carp, and S. grahami, respectively, to estimate an absolute substitution rate. The Ks values were measured with the method as implemented by using the yn00 program in PAML (v4.8) (30).

Putative gene-loss events were traced from the syntenic blocks between zebrafish and the two subgenomes of goldfish. In the triples of consecutive genes within syntenic blocks from the zebrafish genome and two goldfish subgenomes, missing genes were considered as deletions or pseudogenes. Sequences of potential missing genes were confirmed with The BLAST-Like Alignment Tool (BLAT) alignment and mapping coverage of Illumina short reads. Deletions had little support, and pseudogenes contained various defects including premature stop codons, frameshifts, disrupted splicing, and/or partial coding deletions. More details were provided in Supplementary Methods and Analysis 6.

RNA-seq data of six adult tissues, mature eggs, and all embryos with two biological duplicates were mapped to reference genome using Tophat (v2.1.1) (44). Gene expressions in each sample were estimated by RSEM (v1.2.19) (45) and quantified as values of transcripts per million (TPM). Gene expressions with TPM > 0.5 were considered to be detectable. Then, we analyzed expression variation among homoeologous genes in 15 developmental stages by developing coexpression networks with WGCNA (v1.63) (34), following the workflow of Session et al. (9).

We analyzed DNA methylation level of brain and liver tissues from WGBS data using Bismark (v0.19.0) (46) with three steps. More details about the methylation differences in functional elements between two subgenomes are provided in Supplementary Methods and Analysis 8.

Originally posted here:

From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish - Science Advances

Throughout several movies in the Marvel Cinematic Universe, the relationship between Tony Stark and Steve Rogers took center stage. To Chris Evans, the evolution of the two characters that occurred through 2019s Avengers: Endgame was one of his favorite parts of the MCU.

In an interview with theAwards Chatter Podcastby The Hollywood Reporter, Evans discussed his recent role in Apple TV+s miniseries Defending Jacob and his time in the MCU playingSteve Rogers. On the podcast, Evans said that some of his favorite moments in the MCU took place in Avengers: Endgame and involved the scenes between Steve Rogers and Robert Downey Jr.s Tony Stark.

everything from Endgame was really special to me because my headspace was very much in the reflective, grateful part of it. You almost feel like youre living in a memory; you feel like its almost like the moments already passed, so youre really just trying to soak it in and just appreciate what this journey has been like, Evans said.

He continued, Like I said, in Endgame, there are just so many great moments. I love scenes with Downey. I love seeing the evolution of those two characters. They usually give Cap great motivational speeches and things like that. Any of those scenes where theres all of us together, and it just is a real reflective and special moment.

RELATED: The Phone Call From Robert Downey Jr. That Changed Chris Evans Life Forever

While Evans loved working on Avengers: Endgame and the evolution between Steve Rogers and Tony Stark, he told the Awards Chatter Podcast that his favorite scene in the MCU actually occurs in Captain America: The Winter Soldier.

The Russos are real, real cinephiles, and they have such knowledge and love for certain scenes in certain movies. And you can tell when they get excited about certain moments that they want to make iconic; they were really excited about that first elevatorfight scene inWinter Soldier, Evans said on the Awards Chatter Podcast. You could tell that they wanted it to be special, and as a result, thats one of my favorite fight sequences.

When Evans was offered the role of Captain America in the MCU, he was hesitant to accept. In fact, he turned down the role multiple times.

The problem was initially, it was a nine-movie contract. And they said, if these movies take off and do very well, and my life changes and I dont respond well, I dont have the opportunity to say, listen, I need a f*cking break. That just scared me, Evans told Variety in 2014. They called back and they tweaked the deal. It went from nine (films) to six. I said no again.

To help try and convince him to take the role, Downey Jr. called Evans.

I remember getting on the phone with him and strongly suggesting that he not shrink away from the offer, Downey said. I said, Look man, you might not like the fact that youve played one of these guys before (in Fantastic Four), but you know, the thing is this can afford you all sorts of other freedoms I also thought he was the perfect guy for the job.

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Chris Evans Loved 'the Evolution' Between Iron Man and Captain America in the MCU - Showbiz Cheat Sheet

Kareena Kapoor Khans flashback photos prove that the diva hasnt changed a bit and ages like fine wine.

Age is just a number when it comes to the Kapoor sisters. They truly age like fine wine and when it comes to Bebo, she looks like the finest bottle of wine there is. In this new Then vs Now segment, we often look back at the celebritys style and how it has evolved over the years. These throwbacks are generally for us to see how far the leading ladies of B-Town have come.

However, things changed when we took a look back at the Begum of Bollywoods photos and to our surprise, we found no stark difference.

THEN

The ever-glamorous Bebo has always been glowing. The diva has managed to maintain the same even after years passing by. Her signature smudged kohl look has still managed to make the same impact it did years ago. Adding to it, she often resorted to metallic lips which if we look back now seems a bit icky. However, then, she was definitely on-trend.

This one award function look in 2004, however, seems off as she stepped out in an embellished kurta and left her highlighted waves open in a haphazard manner.

Coming to her clothes, mini skirts and bodycon dresses were definitely her go-to. She was often seen in different versions and colours of it. Casual tees and jeans were something she seemed to be most comfortable in.

NOW

Her style now has definitely matured. Fashion pieces and creations are strategically selected so she looks her best. While solid colours still remain to be her go-to, Kareena is still seen in her casual jeans and t-shirt. What has evolved is her ability to experiment with her attires. From different hairdos to clothing, she is often seen bringing new things to the table.

What are your thoughts about her style? Let us know in the comments section below.

For more Fashion & Beauty updates: Follow @pinkvillafashion

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Then Vs Now: Kareena Kapoor Khan's evolution proves her GLAM is on point no matter the decade - PINKVILLA

Number nine shirts are among the most iconic and coveted numbers in football.

And since the dawn of the 21st century, Huddersfield Town have had a wide variety of players to have donned the jersey.

Some only wore it for just a season, while others had it for campaign after campaign, while there's even one player to have had it across a couple of spells at the John Smith's Stadium.

Here's our list of those players to have worn Town's number nine since 2000:

Huddersfield entered the new century with Stewart wearing the club's number nine shirt.

However, his time at Town donning the coveted jersey in the new millennium lasted only a month as, with 15 goals to his name that season by the end of January, he was controversially sold to Division One rivals Ipswich Town for 2.5m.

He helped the Tractor Boys reach the top flight via the play-offs as Town missed out by finishing eighth that season.

He later moved to Sunderland in 2002 before being transferred to Bristol City in 2005.

During that time, he had loan spells at Preston North End and Yeovil Town, before joining the Glovers permanently in 2007.

He stayed there until 2008 and ended his playing days with three seasons at Exeter City before retiring in 2011. He is currently assistant manager to Darrell Clarke at Walsall.

Smith inherited the number from Stewart after his controversial sale to Ipswich Town.

He joined Town from Sheffield United and stayed until 2003, when he joined Northampton Town after the Terriers suffered relegation.

Smith held the number nine shirt from 2000 until the end of the 2001/02 season.

After leaving the Cobblers, Smith also had spells at Darlington, Blyth Spartans and Kettering Town before retiring.

Booth came through the ranks at his hometown club and made his debut in March 1992.

His exploits in front of goal led to him being bought by fellow Yorkshire side Sheffield Wednesday in the summer of 1996 for some 2.7m.

As well as a brief spell on loan at Tottenham Hotspur in 2001, he made the return to Town from Hillsborough in March of that year, though his efforts could not stop Huddersfield being relegated to English football's fourth tier.

The following season, Booth took up the number nine shirt this century for the 2002/03 campaign, in which he found the back of the net six times in more than 30 games as Town were promoted.

After this season, the number nine shirt passed to Pawel Abbott, but Booth remained at Town until he retired in 2009. He remains at the club as an ambassador.

Abbott initially joined Town on loan from Preston North End in 2004 to replace Jon Stead after he was sold to Premier League Blackburn Rovers.

He scored four goals in six games during his loan spell, and was bought by Town on a permanent basis on the back of his good form.

Overall he scored more than 40 times in over 100 appearances for Huddersfield.

He wore the number nine shirt during this time before a move to Swansea City where he was sold in the January transfer window in 2007.

The Jamaica international joined Town on a three-year-deal from Watford in 2009.

He took up the number nine shirt and had a productive campaign as he scored 16 times in 43 games in all competitions.

Robinson made only a handful of appearances for Huddersfield in the 2010/11 season and moved to Milwall on loan in September 2010, later joining the London side permanently.

He had a brief return to Town in 2013 on loan from Derby County and his past clubs include Doncaster Rovers, Scunthorpe United, Motherwell, Port Vale and Swindon Town.

Robinson is currently contracted to Southend United but has been on loan at Colchester United in League Two this campaign.

Two spells with Town this decade for the forward and on both occasions he wore the number nine.

Cadamarteri first signed for Huddersfield in 2007 and joined after being released by Leicester City.

He left the Terriers after two seasons and scoring six times in 51 games, heading north of the border to join Dundee United in the SPL.

Two seasons later, he rejoined Town in January 2011 and ended up staying for a further year-and-a-half in West Yorkshire, before leaving for good when he was not offered a new deal in the summer of 2012 by then-Terriers boss Simon Grayson.

After two seasons at Carlisle United, Cadamarteri hung up his boots in 2014 due to a knee injury.

After joining Town in 2009 from non-league Gateshead, Novak would have to wait until his final season with the Terriers until he donned the number nine shirt.

He was Huddersfield's number nine in the 2012/13 campaign, and in total scored six times in nearly 40 appearances across all competitions that season.

He departed the Yorkshire side in the summer of 2013 when his contract expired and linked up with former Town boss Lee Clark once more at Birmingham City.

He joined Chesterfield on loan during his time at St Andrew's and has since played for Charlton Athletic and Scunthorpe United. He is currently at League Two side Bradford City.

Vaughan joined Huddersfield initially on loan from Norwich City in 2012 and was initially handed the number 18 shirt and scored 14 times.

It was only when he joined the club permanently during the following summer transfer window from the Canaries that he took up the number nine.

He stayed at the John's Smith's Stadium for more than two further seasons by which time he had scored 33 goals in 95 games.

After joining hometown club Birmingham City on loan in November 2015, he joined the Blues permanently in 2016.

Since then, the now 31-year-old has had a host of clubs, including Bury, Sunderland, Wigan Athletic, Portsmouth and Bradford City, and is currently on loan at League One side Tranmere Rovers.

The current wearer of Town's number nine has done so since he joined the club in 2016.

It had been vacant during much of the 2015/16 season following the departure of Vaughan from the Terriers to hometown club Birmingham City.

DR Congo international Kachunga first became a Town player in 2016 when he was signed by David Wagner on a season-long loan from FC Ingolstadt in Germany.

His 13 strikes in all competitions that season helped Huddersfield win promotion to the Premier League via the play-off final victory against Reading, also ending the campaign as Town's top scorer.

Kachunga spent two seasons in the Premier League with Town but only has one goal in the top flight to his name against Watford. This season, the forward has found the back of the net just twice so far.

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Who wore it best? - The evolution of Huddersfield Town's number nine shirt this century - YorkshireLive

Shares in Evolution Petroleum (ASQ:EPM) are currently trading at 2.44, but a key question for investors is how much the current economic uncertainty will affect the price.

One way of making that assessment is to look at the profile of the stock to see where its strengths are. Evolution Petroleum is a player in the Oil & Gas sector. The good news is that it scores well against some important financial and technical measures. In particular, it has strong exposure to two influential drivers of investment returns: high quality and a relatively cheap valuation.

To understand where that shows up, here's a closer look:

GET MORE DATA-DRIVEN INSIGHTS INTO ASQ:EPM

Good quality stocks are loved by the market because they're more likely to be solid, dependable businesses. Profitability is important, but so is the firm's financial strength. A track record of improving finances is essential.

One of the stand out quality metrics for Evolution Petroleum is that it passes 5 of the 9 financial tests in the Piotroski F-Score. The F-Score is a world-class accounting-based checklist for finding stocks with an improving financial health trend. A good F-Score suggests that the company has strong signs of quality.

While quality is important, no-one wants to overpay for a stock, so an appealing valuation is vital too. With a weaker economy, earnings forecasts are unclear right across the market. But there are some valuation measures that can help, and one of them is the Earnings Yield.

Earnings Yield compares a company's profit with its market valuation (worked out by dividing its operating profit by its enterprise value). It gives you a total value of the stock (including its cash and debt), which makes it easier to compare different stocks. As a percentage, the higher the Earnings Yield, the better value the share.

A rule of thumb for a reasonable Earnings Yield might be 5%, and the Earnings Yield for Evolution Petroleum is currently 17.5%.

In summary, good quality and relatively cheap valuations are pointers to those stocks that are some of the most appealing to contrarian value investors. It's among these shares that genuine mis-pricing can be found. Once the market recognises that these quality firms are on sale, those prices often rebound.

Finding good quality stocks at attractive prices is a strategy used by some of the world's most successful investors. If you want to find more shares that meet these rules, you can see a comprehensive list on Stockopedia's StockRanks page.

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Two factors that could drive the Evolution Petroleum share price higher - Yahoo Finance UK

Evolution, theory in biology postulating that the various types of plants, animals, and other living things on Earth have their origin in other preexisting types and that the distinguishable differences are due to modifications in successive generations. The theory of evolution is one of the fundamental keystones of modern biological theory.

The diversity of the living world is staggering. More than 2 million existing species of organisms have been named and described; many more remain to be discoveredfrom 10 million to 30 million, according to some estimates. What is impressive is not just the numbers but also the incredible heterogeneity in size, shape, and way of lifefrom lowly bacteria, measuring less than a thousandth of a millimetre in diameter, to stately sequoias, rising 100 metres (300 feet) above the ground and weighing several thousand tons; from bacteria living in hot springs at temperatures near the boiling point of water to fungi and algae thriving on the ice masses of Antarctica and in saline pools at 23 C (9 F); and from giant tube worms discovered living near hydrothermal vents on the dark ocean floor to spiders and larkspur plants existing on the slopes of Mount Everest more than 6,000 metres (19,700 feet) above sea level.

The virtually infinite variations on life are the fruit of the evolutionary process. All living creatures are related by descent from common ancestors. Humans and other mammals descend from shrewlike creatures that lived more than 150 million years ago; mammals, birds, reptiles, amphibians, and fishes share as ancestors aquatic worms that lived 600 million years ago; and all plants and animals derive from bacteria-like microorganisms that originated more than 3 billion years ago. Biological evolution is a process of descent with modification. Lineages of organisms change through generations; diversity arises because the lineages that descend from common ancestors diverge through time.

The 19th-century English naturalist Charles Darwin argued that organisms come about by evolution, and he provided a scientific explanation, essentially correct but incomplete, of how evolution occurs and why it is that organisms have featuressuch as wings, eyes, and kidneysclearly structured to serve specific functions. Natural selection was the fundamental concept in his explanation. Natural selection occurs because individuals having more-useful traits, such as more-acute vision or swifter legs, survive better and produce more progeny than individuals with less-favourable traits. Genetics, a science born in the 20th century, reveals in detail how natural selection works and led to the development of the modern theory of evolution. Beginning in the 1960s, a related scientific discipline, molecular biology, enormously advanced knowledge of biological evolution and made it possible to investigate detailed problems that had seemed completely out of reach only a short time previouslyfor example, how similar the genes of humans and chimpanzees might be (they differ in about 12 percent of the units that make up the genes).

This article discusses evolution as it applies generally to living things. For a discussion of human evolution, see the article human evolution. For a more complete treatment of a discipline that has proved essential to the study of evolution, see the articles genetics, human and heredity. Specific aspects of evolution are discussed in the articles coloration and mimicry. Applications of evolutionary theory to plant and animal breeding are discussed in the articles plant breeding and animal breeding. An overview of the evolution of life as a major characteristic of Earths history is given in community ecology: Evolution of the biosphere. A detailed discussion of the life and thought of Charles Darwin is found in the article Darwin, Charles.

Darwin and other 19th-century biologists found compelling evidence for biological evolution in the comparative study of living organisms, in their geographic distribution, and in the fossil remains of extinct organisms. Since Darwins time, the evidence from these sources has become considerably stronger and more comprehensive, while biological disciplines that emerged more recentlygenetics, biochemistry, physiology, ecology, animal behaviour (ethology), and especially molecular biologyhave supplied powerful additional evidence and detailed confirmation. The amount of information about evolutionary history stored in the DNA and proteins of living things is virtually unlimited; scientists can reconstruct any detail of the evolutionary history of life by investing sufficient time and laboratory resources.

Evolutionists no longer are concerned with obtaining evidence to support the fact of evolution but rather are concerned with what sorts of knowledge can be obtained from different sources of evidence. The following sections identify the most productive of these sources and illustrate the types of information they have provided.

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evolution | Theory, Examples, & Facts | Britannica

Charity Nebbe speaks with biologists Maurine Neiman and Jim Colbert.

While schools are closed, we're creating a series of "Talk of Iowa" episodes that will be fun and educational for learners of all ages.Every Tuesday, we'll learn about biology, and every Thursday, we'll learn about Iowa history.

On this edition ofTalk of Iowa biologists Maurine Neiman and Jim Colbert will introduce listeners to the theory of evolution.

Think for a moment about the dizzying number of plant and animal species you know about. Life on Earth is incredibly diverse, and it's all because of evolution.

Neiman and Colbert give us a short course in evolution basics. We also debunk some common myths about evolution. Evolution is not purposeful, always positive or always in the direction of greater complexity.

We also hear about some examples of amazing adaptations and weird traits, or maladaptations. We learn why evolution is important to each one of us. Later in the program, we learn a little bit about how viruses evolve, resulting in new threats to human health.

Vocabulary:

Discussion questions & activities:

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How Did We Get Here? A Look At The Theory Of Evolution - Iowa Public Radio

Live dealer specialist Evolution Gaming has struck a strategic agreement with Golden Nugget that will see it expand the range of games provided to the US casino operator.

Golden Nugget was the first operator in New Jersey to launch live dealer games in 2016, in partnership with Ezugi, a supplier acquired by Evolution in November 2018.

Since then the operator has continued to offer games broadcast from a dedicated studio run by Ezugi, which also provides content to partners such as BetMGM, PartyCasino, Caesars and FanDuel.

Under the expanded agreement, it will now add Evolutions portfolio of US live casino services to its offering. This will make game types such as Dream Catcher, Side Bet City and Top Card available on its New Jersey site, streamed live from its Atlantic City studio, or from Golden Nuggets existing facilities.

Furthermore, clients of that studio will also have the option to access Evolutions content through their existing partnership. While the agreement currently focuses on New Jersey, the only state in which Golden Nugget offers igaming currently, there is an option to expand into other markets as regulation permits.

Read the full story on iGB North America.

Link:

Evolution seals strategic partnership with Golden Nugget - iGaming Business

In the year 2000 Hyundai Motor introduced its first-generation Santa Fe, making the company one of the pioneers in the SUV market.

Now celebrating its 20thanniversary, the Santa Fe has become an icon for the brand, and Hyundai is taking a look back at how its first SUV has evolved over the years.

Having entered dealerships in 2001, Santa Fe is Hyundais longest-running model in Europe. Now in its fourth generation, the Santa Fe has undergone significant evolution in its design, safety and technology over the years, often leading the way as a flagship for new features. This summer, Hyundai will launch an enhanced version of the current generation with new electrified powertrains and major design updates.

Following its launch two decades years ago, Santa Fe quickly became one of Hyundais most popular models. Named after a city in the Southwestern U.S., it was the companys first SUV, and played an important role in establishing Hyundai in the SUV segment. Unusually for a Hyundai model, the Santa Fe has its own logo showing the model name and a sun, while its name has been carried over to future generations, continuing its heritage. Over the past 20 years, Hyundai has sold more than 5,260,000 units of Santa Fe globally.

The Santa Fe was Hyundais first SUV, and it is one of our longest-running model lines, making it a key model not only globally, but also in Europe. For Hyundai it is an automotive icon which continues to evolve in terms of design, technology, roominess and comfort. With this latest evolution, Santa Fe maintains its status as a flagship model in our broad SUV portfolio, and further underlines our heritage in SUVs while also moving the game forward with its innovation and electrification.

Andreas-Christoph HofmannVice President Marketing & Product at Hyundai Motor Europe

First-generation Santa Fe (2000-2006): the original best-seller

Hyundai introduced the Santa Fe to European audiences for the first time at the 2000 Geneva Motor Show. While subsequent generations became progressively premium over time, the very first Santa Fe was practical and appreciated for its functionality and reliability. In 2001, not long after the first model was produced Hyundai had to ramp up production due to the overwhelming demand in the US.

The first generation Santa Fe featured a rugged, yet refined look and was substantially longer and wider than many of its rivals in the segment, emphasising its practicality for off-road driving. The spacious interior offered enough room for up to five passengers, as well as ample cargo space. Meanwhile, its convenience features, which included air conditioning, a CD player, as well as electric windows, mirrors and a sunroof, were comprehensive for the time.

In 2003, in response to customer demand for even more driving performance, Hyundai upgraded Santa Fe with a more powerful engine and a computer-controlled four-wheel drive system.

Second-generation Santa Fe (2006-2012): more power, more space, and an updated safety system

The second-generation Santa Fe was launched at the North American International Motor Show in January 2006. It featured a new 2.2-liter diesel-powered engine and an updated 2.7-liter gasoline-poweredV6 while offering significantly improved handling and sportier engines to equip customers for a range of driving and weather conditions.

By the middle of the 2000s, design was becoming increasingly important to customers. Therefore, the Santa Fes successor model featured significant changes outside and inside the vehicle. Its exterior offered an assertive front grille, confident sculpted lines and finely detailed headlights. This contemporary look showcased how the brands design direction was evolving.

The interior utilised a range of soft-touch, high-quality materials and low-gloss surfaces to provide second-generation Santa Fe customers with a touch of luxury. This premium feeling was further emphasised by the blue backlighting which surrounding the models controls and switches, in combination with leather upholstery. Meanwhile, it offered more space than before, as for the first time, the option of adding a third row of seats was available, extending the five-seater to a seven-seater.

With customers of the time demanding increased safety features, the second-generation Santa Fe offered a series of extensive safety upgrades, which continued Hyundais leadership in standardising the industrys most effective technologies. Electronic Stability Control (ESC), an anti-lock braking system (ABS), side-curtain airbags for all seating rows, a tyre pressure monitor, and active front head restraints now came as standard. Later, a premium version was added, which included a built-in navigation system, rear-view camera, cruise control and a light sensor.

Third-generation Santa Fe (2012-2018): enhanced safety and improved connectivity

The third-generation Santa Fe was a big step forward for Hyundai, as it offered even greater comfort and quality, re-tuned engines and improved efficiency. In addition, it featured a new design direction called Storm Edge, which consisted of refined lines as well as bold and voluminous surfaces. By adding a more emotional, muscular look and a wealth of premium features, the company demonstrated it was moving away from offering a purely functional SUV, and instead a sophisticated lifestyle vehicle.

Available as both a sporty five-seater and a version with a long wheelbase offering three rows of seats for six or seven passengers, the third-generation Santa Fe also boasted a refreshed unibody crossover platform. The long version received a slightly differentiated design, including a unique hexagonal grille design, a new look for the B-pillar, optional 19-inch alloy wheels and flush dual exhaust tips. This illustrated that, in addition to maintaining the earlier models strengths of practicality, roominess and dependability, the new model looked modern and dynamic, making it an ideal proposition for to conquest new customers to the Hyundai brand.

Both Santa Fe models offered a similar interior look, fully geared towards passenger comfort and functionality. In the early 2010s, advances in technology gave automakers the opportunity to improve their customers comfort and driving experience with a range of intelligent connectivity features. As a result, the third-generation Santa Fe offered an optional multifunction eight-inch touchscreen with navigation with a simpler and more intuitive user interface as well as enhanced voice recognition commands, while phone connectivity was also improved.

With the third generation Santa Fe, Hyundai reinforced its commitment to providing its customers with class-leading safety features. These included a premium braking package, which contained four-wheel disc brakes, an Anti-Lock Braking System (ABS) including Brake Assist providing maximum braking force when a panic stop is detected, and Electronic Brake-force Distribution (EBD) to automatically adjust the braking force to front and rear axles based on vehicle loading conditions. By offering these levels of state-of-the-art active safety technology, the third-generation model ensured improved protection for drivers, passengers and pedestrians.

Fourth-generation Santa Fe(2018-present): SmartSense safety features and a bold new design

Building on the success of its previous generations, in 2018 Hyundai introduced the fourth-generation Santa Fe. Its premium feeling is illustrated by its prestigious appearance, while it is equipped with the most advanced technology as well as best-in-class safety features and exceptional roominess.

The elegant SUV model features a bold outward appearance with a wide, athletic stance. Hyundais signature Cascading Grille decorates the front, and the side is enhanced by sleek lines which stretch along the roof and from the headlights to the taillights. This reinforces the cars status at the top of Hyundais SUV line-up. Inside, it is the roomiest Santa Fe yet, with 38 mm more leg room in the second row.

Equipped with Hyundais latest SmartSense technology, the fourth-generation Santa Fe is among the safest in its class, and it received the maximum five-star safety rating from Euro NCAP. Hyundai demonstrates it continues to care for its customers by offering even more innovative features, including Hyundais in-house developed and industry-first Rear Occupant Alert, which uses an ultrasonic sensor to detect the movement of children or pets on the rear seat and alert the driver when leaving the car.

Another safety feature is Rear Cross-Traffic Collision-Avoidance Assist, which scans a 180-degree area behind the vehicle, warning the driver and applying the brakes if necessary to avoid collisions. Additionally, for the first time in a Hyundai, the fourth-generation Santa Fe features a full head-up display that projects relevant information onto the windshield to keep the view clear while driving.

The All-New Santa Fe features HTRAC, Hyundais advanced four-wheel drive system with an enhanced torque application depending on wheel grip and the speed of vehicle. It supports drivers in all kinds of driving situations, whether on snow, slippery roads or in regular road conditions, and enhances stability in cornering.

18 years after the introduction of the first-generation model, this powerful, elegant SUV has evolved to become Hyundais premium flagship model in Europe. The continuing improvements the Santa Fe has undergone over the past two decades demonstrate Hyundais commitment to developing quality products with the latest features for its customers. Further details on the enhanced fourth generation will be revealed in the near future.

SOURCE: Hyundai

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Two decades of the Hyundai Santa Fe: evolution of an automotive icon - Automotive World

This story appeared in the June 2020 issue as "Head Cases."Subscribeto Discover magazine for more stories like this.

These are heady times for paleoanthropologists. In the opening decades of the 21st century, new discoveries have refined and revised the story of human evolution at an unprecedented rate.Researchers have added four new members to the genus Homo: South Africas Homo naledi, Asias Denisovans, Indonesias hobbit H. floresiensis and, just last year, its neighbor in the Philippines, H. luzonensis. Improvements in extracting and analyzing ancient DNA and preserved proteins have created molecular-level tools capable of determining relationships between both individuals and species.

Much of the new research involves high-tech analysis of fragmentary fossils or genetic code but no single tooth, scrap of finger bone or shiny piece of lab equipment captures our attention quite like a skull.

The head, and especially the face, is the part of a person that we most commonly engage with, and also usually self identify with, says University of Tbingen paleoanthropologist Katerina Harvati, who co authored a 2019 study in Nature Ecology & Evolution on the evolutionary history of the human face.

Fossil skulls, she says, have the ability to convey not only a lot of information about the species to scientists, but also can give an immediate, intuitive impression of what an individual would have been like as a person when alive and can therefore more easily capture the imagination of both scientists and the public.

And that, quite frankly, is where things get messy.

Christoph Zollikofer, an anthropologist at the University of Zurich, cautions that the sheer charisma of fossil skulls of being face-to-face with an individual who lived thousands or even millions of years ago can lead even the professionals astray.

Our mindsets are like shop display windows that separate us from the mannequins: We look at these fossil skulls through our own mirror images and imaginations, Zollikofer says.

When researchers with different visions look at the same ancient skull, often heated debates erupt. Such arguments have become more common in the 21st century with the discovery of each new fossil that challenges conventional thinking about the evolution of hominins humans and our nearest ancestor and kin species. The more fossils paleoanthropologists find, and the more methods they have to study them, the murkier the story of human evolution seems.

When there were few fossils, it was very easy to make a line and show a very linear evolution, says Silvana Condemi, a paleoanthropologist at Aix-Marseille University in France and co-author of A Pocket History of Human Evolution: How We Became Sapiens. Now we have a lot more fossils, and we see its not so simple, it was much more complex, but we dont have enough fossils to understand it.

She adds: We have new tools. We try to be rigorous. We do our best. But a single discovery can still change everything.

Five fossil skull finds, each with its own controversy, provide a glimpse into how much weve learned about our origin story and how much remains uncertain.

(Credit: Didier Descouens/Wikimedia Commons)

Specimen: Touma

Species: Sahelanthropus tchadensis

Age: up to 7 million years old

Found: Chad, Central Africa

First described: 2002

Discovered in 2001 in Northern Chads desert landscape, the find was extraordinary: a collection of bones and bone fragments sitting beside a mostly complete skull. Researchers named the skull Touma, or hope of life in the local language. Its features were a mashup of old and new, a chimp-sized brain but with small canine teeth theyre typically smaller in hominins than in chimps, our nearest living relatives.

It was the fossils age that was even more shocking, however. Touma is between 6 million and 7 million years old. At the time, paleoanthropologists believed that the last common ancestor we share with chimps was at least a million years younger. Touma suggested the split in our lineages occurred much earlier than thought. And, for many paleoanthropologists, one feature in particular suggested that Touma was one of us, the first hominin. The foramen magnum is the opening at the base of the skull where the spinal cord exits. The angle of the opening can reveal if the spine stretched out behind the skull, as it does for four-legged animals, or dropped down, like it does for bipedal hominins.

According to the reconstruction, the foramen magnum is in a position that suggests it was able to walk on two feet, Condemi says of Touma. Bipedalism is one of the essential features of Homo. This species was in that line.

Touma was hailed as the oldest known hominin, giving researchers a look at the very roots of our lineage in the Late Miocene, when our ancestors split from other apes. When the cranium came out, paleoanthropologists looked at it and said, It must be The One, says paleontologist Fred Spoor of the Natural History Museum in London. Then there was pushback from the Miocene ape [research] community saying, Wait a minute.

As more Miocene ape fossils turn up, the overall picture becomes more complex. In 2019, for example, separate reconstructions of hips and torsos of European Miocene apes Danuvius and Rudapithecus definitely not hominins suggested they also might have been at least experimenting with some form of bipedalism.

Its not a given that only hominins were bipedal, says Spoor. We may well end up in a situation where there were bipedal Miocene apes We shouldnt assume that everything in the past has a lineage that continues in the present.

Zollikofer was the lead author on a 2005 reconstruction, published in Nature, of the Touma skull based on high-resolution CT scans. His team concluded that Toumas species, Sahelanthropus, was more closely related to hominins than to apes. But the researchers were less certain about how it moved.

It is clear that its skull shows evidence for some form of upright stance and bipedal locomotion, says Zollikofer. Is Sahelanthropus our ancestor? We will never know! He might have been part of a population of bipedal apes that was an evolutionary dead end.

Spoor sees Touma as a key specimen regardless of whether it belongs in our family tree. The importance of the cranium is immense. Its a 7-million-year-old fossil that is well preserved, he says. The fairest way to describe it is as the earliest possible or potential hominin. If its not a hominin, its likely quite close.

(Credit: ALe Omori/Cleveland Museum of Natural History)

Specimen: MRD

Species: Australopithecus anamensis

Age: 3.8 million years old

Found: Ethiopia, East Africa

First described: 2019

About 4.2 million years ago, the first australopiths, predecessors of our own Homo genus, emerged. Their brains were a little larger than those of a chimp, but not by much, and they were bipedal. The most famous hominin fossil, 3.2-million-year-old Lucy, was a member of Australopithecus afarensis, a later member of the genus. It was A. afarensis, conventional thinking went, that diversified into other australopith species spread across much of Africa.

Many researchers believed that A. afarensis itself evolved about 3.9 million years ago from the first australopith, A. anamensis. Partial fossils of this earlier species had been found at multiple sites in East Africa, but paleoanthropologists just couldnt put a face to the name. Even fragmentary skull fossils from A. anamensis were scarce.

In August, however, researchers revealed a jawdropping find from Ethiopia: a nearly complete skull of A. anamensis.

Anamensis we have known for decades, but this was the first time we had the cranium, says Condemi, who was not involved in the research. Its wonderful to have an idea what it looks like.

We learn the skull was very small, just a little bigger than Sahelanthropus. The face had chimplike features, with a big sagittal crest, she adds, referring to a ridge of bone along the top of the skull that is more pronounced in animals with powerful jaw muscles, which attach to the crest.

Theres just one problem: The skull, called MRD, is 3.8 million years old. Thats about 100,000 years younger than the oldest fossil described as A. afarensis. MRD, according to the researchers who discovered it, nixed the idea that, over time, A. anamensis had evolved into A. afarensis. Instead, the two species appear to have co-existed.

The idea that anamensis led to afarensis has been thrown out the window though not entirely, says Spoor, who was not part of the team.

To the casual observer, the distinction may seem minor, but understanding the course of australopith evolution has direct consequences for charting our own story.

Spoor and other experts focus on the smallest details, such as the angle of projection of the cheekbone, to see the bigger picture of how the hominin family tree grew to include at least six australopith species and, eventually, the genusof Homo.

"To understand how to build the tree, you have to understand what is newly evolved and what is inherited, says Spoor. The new skull gives us the opportunity to think about all that and to reconsider that all these [later] groups originated from anamensis and not afarensis.

He adds an important caveat: The MRD teams conclusions that the two species overlapped are based on the assumption that the oldest fossil classified as A. afarensis a fragment of skull dated to 3.9 million years ago actually belongs to that species.

Zollikofer shares that concern: The interpretation as having two species at the same time suffers from the fact that there are only two specimens. How can we know for sure what is within-group and betweenspecies variation here? We cant.

Until additional skulls of both A. anamensis and A. afarensis turn up, say the researchers, MRD may be just a pretty face.

(Credit: Guram Bumbiashvili/Georgian National Museum)

Specimen: Skull 5

Species: Homo erectus

Age: 1.77 million to 1.85 million years old

Found: Georgia, Caucasus Region of Eurasia

First described: 2013

A day's drive south of the Caucasus Mountains in the country of Georgia, beside a ruined medieval fortress and a small working monastery, sits one of the worlds most important, and confounding, paleoanthropological sites: Dmanisi, home to the oldest hominin fossils outside Africa.

Beginning in the 1980s, researchers unearthed thousands of fossils that are about 1.8 million years old. Among the remains of Etruscan wolves, saber-toothed tigers, deer and other animals are the bones of several hominins, including partial and complete skulls.

A particularly robust lower jaw was found in 2000 and initially described as an entirely new species, H. georgicus. In 2013 in Science, however, researchers announced theyd unearthed the rest of the individuals skull, now known as Skull 5. Having the complete skull led the team to do an about-face, no pun intended. They concluded the Dmanisi hominins were members of H. erectus, the earliest member of our genus found beyond Africa.

What led to the researchers unusual reversal? As Zollikofer puts it, Skull 5 is not alone It has four buddies, and all of them look quite different from each other.

Zollikofer has co-authored several Dmanisi hominin studies, including a 2006 paper in The Anatomical Record Part A on one of the other skulls. That specimen is unique in the entire hominin fossil record: The individual lost its teeth several years before death, leaving it unable to chew. It may have survived with assistance from others, suggesting social behavior otherwise unknown this early in human evolution.

It was the 2013 study on Skull 5, however, for which Zollikofer served as senior author, that ignited an academic firestorm. In addition to reclassifying the Dmanisi hominins as H. erectus, the team went a step further: They suggested that differences between the five Dmanisi skulls offered proof of considerable variation within H. erectus, so much so that other early Homo species, such as Africas H. habilis, could be reclassified as H. erectus.

It was a fresh salvo in one of paleoanthropologys longest-running battles: Was the early evolution of Homo linear, a single species changing over time into a new species? Or was it an unruly tangle of multiple populations, species and subspecies, mixing and mingling, sometimes evolving in isolation and then coming together again to interbreed?

Numerous critics took on the teams conclusions, including Spoor, who authored the provocatively titled Nature commentary Small-brained and big-mouthed.

Spoor appreciates Skull 5s significance It is a beautiful example of a very early Homo erectus but remains opposed to the teams radical proposal to redefine all early Homo species as H. erectus. He notes that their conclusion hinges on the assumption that the five Dmanisi skulls, found in the same general layer of rock, lived at the same time.

One level of excavation can represent 10,000, 20,000 years, Spoor says.

Being able to document the variation between Skull 5 and other Dmanisi hominins may be the most significant thing about the fossils. Exactly what that significance is, however, varies from one researcher to the next.

A reconstruction, based on partial bones that are about 315,000 years old, shows facial features within the range of modern humans. (Credit: Sarah Freidline/MPI Eva Leipzig)

Specimen: Irhoud 10

Species: Homo sapiens

Age: about 315,000 years old

Found: Morocco, North Africa

First described: 2017

For decades, conventional thinking was that H. sapiens emerged no more than 200,000 years ago, and in East Africa. Then a team took another look at a minor fossil site in Morocco.

In 1961, during mining operations, workers digging into a hillside had found an old skull. Subsequent excavations turned up more partial fossils, but the species was as uncertain as their estimated age, which ranged from 40,000 to 160,000 years old.

The most recent round of digging at the site, known as Jebel Irhoud, began in 2004 and included a more rigorous approach to dating the additional fossils found. The results were striking: The hominins, which included a partial face and braincase known as Irhoud 10, were about 315,000 years old.

In 2017 in Nature, researchers announced that Irhoud 10s facial features were within the range of modern humans. The Moroccan hominins were, said the authors, the oldest H. sapiens in the fossil record by more than 100,000 years.

This material represents the very root of our species, lead researcher Jean Jacques Hublin told media at the time.

Other paleoanthropologists saw the teams conclusions as hype.

Paleoanthropologists have an obsession with species, species definitions and ancestors, says Zollikofer, noting that Darwin believed there was far more fluidity among related populations. In Jebel Irhoud you can focus on a set of facial features that create a link to H. sapiens, or focus on other features that create a strong link to earlier humans. Guess which option sells better?

Chief among the archaic features of the Irhoud hominins is the low and elongated braincase, far from the rounded shape thats a hallmark of modern H. sapiens. But others in the field see the Irhoud hominins as an exciting snapshot of evolution in action.

I consider Jebel Irhoud Homo sapiens, says Condemi. What we see in Jebel Irhoud is similar to what we see in the evolution of Neanderthals, in that the Neanderthal we see from 200,000 years ago is not the Neanderthal we see from 50,000 years ago. There is evolution within a lineage.Spoor agrees. Evolution is a continuous event. Different parts of the head evolve at a different tempo. Its neat to see modernity emerge.

While the age of the Irhoud fossils is significant, so is the location. Finding the earliest H. sapiens thousands of miles from East Africa is as unexpected as the Irhoud hominins age.

I think what this evidence shows is that our old model of looking for a specific geographical region where modern humans evolved, a kind of Garden of Eden, so to speak, was probably too simple, says the University of Tbingens Harvati, a co-author of the 2017 paper introducing Irhoud 10. It is much more likely that several closely related populations across Africa contributed to our lineage, at times diverging and coming back together as environmental conditions separated them or brought them back into contact with each other.

I think [Irhoud] means that the cradle of Homo sapiens is not East Africa. Its all of Africa, adds Condemi. It means sapiens is a Pan-African species.

The partial cranium (right) and its reconstruction (left, middle) demonstrate a unique feature of modern humans the rounded shape contrasts sharply with Neanderthals and their ancestors. (Credit: Katerina Harvati/Eberhard Karls University Of Tbingen)

Specimen: Apidima 1

Species: Homo sapiens

Age: about 210,000 years old

Found: Greece, southern Europe

First described: 2019

In 2018, a Partial modern H. sapiens jaw from Israel, known as Misliya-1, pushed back the clock for our first road trip. It was up to 194,000 years old, evidence that our species was venturing out of Africa much earlier than once thought.

Given the general acceptance of Misliya-1, it was perhaps surprising that another fossil, described last July in Nature, met with so much controversy. Known as Apidima 1, the partial skull from Greece had been found more than 40 years earlier but had never been rigorously analyzed. Thats in part because it was discovered within arms reach of another, more complete hominin skull, Apidima 2, a Neanderthal. Found so close to it, Apidima 1 was assumed to be Neanderthal, too.

But then Harvati and her team looked at both skulls and conducted more advanced dating to determine their age. The results surprised even the researchers.

Apidima 2 was about 170,000 years old. But the team concluded that Apidima 1, about 210,000 years old, was H. sapiens: the earliest evidence of our species in Europe by more than 160,000 years.

We thought that Europe was the exclusive realm of the Neanderthals and their ancestors until about 45,000 years ago, says Harvati. However, there is no inherent reason why this should be so. There was no barrier that would have prevented early modern humans already in the Near East to spread further north to Anatolia and southeastern Europe.

And Apidima 1, says Harvati with certainty, is H. sapiens. Even though only a portion of the skull has been preserved, its the back area, which is uniquely rounded in modern humans.

Not everyone shares her confidence.

Says Zollikofer: [Apidima 1] is a conundrum. It could represent a lost aspect of early Neanderthal variation. It could represent a lost human population, without species attribution. It could represent H. sapiens. It is frustrating that it is so badly preserved; on the other hand, just being so badly preserved gives room for imagination.

In fact, just before Nature published Harvatis results, a smaller journal, available only in French, published another study on Apidima 1. Those authors concluded the partial skull belonged to the Neanderthal lineage.

As for the disparity in age between the two fossils, even Harvati first assumed they were contemporaries until results showed otherwise. The partial skulls and other, unidentified bone fragments were preserved in breccia, a mishmash of gravel and random debris washed into and through the cave system and then cemented together over time.

Our current hypothesis is that the specimens both fell into a kind of shaft, which filled with sediments from various parts of the cave, were jumbled together and solidified together, says Harvati.

She plans to return to the cave to conduct fresh excavations. Finding additional fossils may put critics concerns to rest or start new debates.

Spoor, echoing the mindset of many in the field at this thrilling and uncertain time, is ready for the next unexpected fossil find.

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5 Skulls That Shook Up the Story of Human Evolution - Discover Magazine