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Figure 104 from: Maddison WP, Maddison DR, Derkarabetian S, Hedin M (2020) Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini). ZooKeys 925: 1-54. https://doi.org/10.3897/zookeys.925.39691

Figure 104 Relationships among Attulus floricola mitochondrial COI sequences in the context of the floricola group. Specimens in bold had their relationships constrained by the UCE phylogeny of Fig. 48; not shown are the relationships outside the floricola group, which are fixed to match the UCE phylogeny. The placement of non-bold specimens on this constrained skeletal tree was inferred by maximum likelihood (RAxML, codon positions as separate partitions).

Figures 1-14 from: Maddison WP, Maddison DR, Derkarabetian S, Hedin M (2020) Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini). ZooKeys 925: 1-54. https://doi.org/10.3897/zookeys.925.39691

Figures 1-14 Subtribe Aillutticina (1–4) and the Jollas-Tomis clade of the subtribe Sitticina (5–14) 1–4Aillutticus nitens, Uruguay (-34.877, -56.023): 1–3 male 4 female 5, 6Tomis palpalis male and female, Ecuador (-0.1996, -77.7023) 7, 8Jollas species: 7J. cupreus male, Ecuador (-0.675, -76.397) 8Jollas sp. female, Ecuador (-0.7223, -77.6408) 9J. leucoproctus, Uruguay (-34.94, -54.95) 10J. flabellatus, Uruguay (-34.426, -55.195) 11–14Attinella dorsata male (11–13) and female (14), Canada (48.870, -123.379). Also included in the Jollas-Tomis clade is Sittisax (Figs 99–103). Additional members of the Jollas-Tomis clade can be seen in Figs 108–128.

Figures 105-107 from: Maddison WP, Maddison DR, Derkarabetian S, Hedin M (2020) Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini). ZooKeys 925: 1-54. https://doi.org/10.3897/zookeys.925.39691

Figures 105-107 Epigynes of Attinella dorsata and Tomis welchi105 holotype of Attus dorsatus Banks, 1895, epigyne, ventral view 106, 107 holotype of Sitticus welchi Gertsch & Mulaik, 1936 106 epigyne, ventral view 107 cleared vulva, dorsal view.

Figures 129-139 from: Maddison WP, Maddison DR, Derkarabetian S, Hedin M (2020) Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini). ZooKeys 925: 1-54. https://doi.org/10.3897/zookeys.925.39691

Figures 129-139 Chromosomes of first meiotic division in males of the Jollas-Tomis clade 129, 130Attinella concolor, with only seven pairs of autosomes, but each two-armed, 14m+Xm0, Florida (29.63N, 82.37W) 131Tomis manabita, showing the two Xs off to one pole, and 13 acrocentric bivalents on the metaphase plate, Ecuador (0.9S, 80.5W) 132–136Sittisax ranieri, whose distinctive XmXaYm appears as a rabbit head with a droopy ear. White triangles show points where two bivalents are apparently linked together 134–136 details of XXY of S. ranieri137–139Sittisax saxicola, with sex chromsomes, interpreted tentatively as XaXaXaYm, appearing as a rabbit head with three ears, Switzlerland (46.9N, 9.2E).

Figures 108-119 from: Maddison WP, Maddison DR, Derkarabetian S, Hedin M (2020) Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini). ZooKeys 925: 1-54. https://doi.org/10.3897/zookeys.925.39691

Figures 108-119 Jollas cupreus, sp. nov. (except 112, J. puntalara) 108, 109 Left palp of holotype 108 ventral view 109 retrolateral view 110 ventral view of epigyne of paratype 111 dorsal view of same, cleared 112 palp of holotype of J. puntalara Galiano 113–115 holotype male 116 male from Yasuní, Ecuador (-0.675, -76.397) 117 holotype male in alcohol 118, 119 paratype female.

opencc-by-4.0Jan 2010View details →

Figure 1 in Chromosomal separation of difficult species of Copris Geoffroy, 1762 and Onthophagus Latreille, 1802 (Coleoptera, Scarabaeidae), with discussion of O. massai Baraud as a British Pleistocene fossil

Figure 1. Map showing the collection sites of the material used in this paper. See Table 1 for explanation of the numbers, and note that neighbouring sites may share the same number.

opencc-zeroJun 2020View details →

Data from: Shared ancestral polymorphism and chromosomal rearrangements as potential drivers of local adaptation in a marine fish

Gene flow has tremendous importance on local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation, and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of evolutionary mechanisms impending or favoring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (Mallotus villosus). We first assembled a 490 Mbp draft genome of M. villosus to map our RAD sequence reads. Then, we used a large dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they likely diverged from 3.8 to 1.8 MyA and experienced secondary contacts. Within each lineage, our analyses provided evidence for large Ne and high gene flow among spawning sites. Within the NWA lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that, both shared polymorphism among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.

opennotspecifiedMay 2017View details →

Volleth, 1988) in Comparative chromosomal studies in Rhinolophus formosae and R. luctus from China and Vietnam: elevation of R. l. lanosus to species rank

Volleth, 1988)

opennotspecifiedMay 2017View details →

the gonosomes after CBG-banding in Comparative chromosomal studies in Rhinolophus formosae and R. luctus from China and Vietnam: elevation of R. l. lanosus to species rank

the gonosomes after CBG-banding

Figure 7 from: Astuti G, Bedini G, Ciccarelli D, Liu L, Tiburtini M, Peruzzi L (2020) Chromosome numbers for the Italian flora: 9. Italian Botanist 9: 101-110. https://doi.org/10.3897/italianbotanist.9.54973

Figure 7 Pulmonaria officinalis L. subsp. officinalis from Castelmonte (Prepotto, Udine), 2n = 16. Scale bar: 10 μm.

Figure 2 from: Astuti G, Bedini G, Ciccarelli D, Liu L, Tiburtini M, Peruzzi L (2020) Chromosome numbers for the Italian flora: 9. Italian Botanist 9: 101-110. https://doi.org/10.3897/italianbotanist.9.54973

Figure 2 Pulmonaria vallarsae A.Kern. subsp. apennina (Cristof. & Puppi) L.Cecchi & Selvi from Passo del Muraglione (San Godenzo, Firenze), 2n = 22. Scale bar: 10 μm.

Figure 1 from: Astuti G, Bedini G, Ciccarelli D, Liu L, Tiburtini M, Peruzzi L (2020) Chromosome numbers for the Italian flora: 9. Italian Botanist 9: 101-110. https://doi.org/10.3897/italianbotanist.9.54973

Figure 1 Pulmonaria vallarsae A.Kern. subsp. apennina (Cristof. & Puppi) L.Cecchi & Selvi from Molino del Pallone (Sambuca Pistoiese, Pistoia), 2n = 22 (a) and 2n = 28 (b). Scale bar: 10 μm.

Figure 4 from: Astuti G, Bedini G, Ciccarelli D, Liu L, Tiburtini M, Peruzzi L (2020) Chromosome numbers for the Italian flora: 9. Italian Botanist 9: 101-110. https://doi.org/10.3897/italianbotanist.9.54973

Figure 4 Pulmonaria vallarsae A.Kern. subsp. vallarsae from Bellaria di Cei (Villa Lagarina, Trento), 2n = 22. Scale bar: 10 μm.

Figure 3 from: Astuti G, Bedini G, Ciccarelli D, Liu L, Tiburtini M, Peruzzi L (2020) Chromosome numbers for the Italian flora: 9. Italian Botanist 9: 101-110. https://doi.org/10.3897/italianbotanist.9.54973

Figure 3 Pulmonaria vallarsae A.Kern. subsp. vallarsae from Pian delle Fugazze (Vallarsa, Trento), 2n = 22. Scale bar: 10 μm.

Figure 8 from: Astuti G, Bedini G, Ciccarelli D, Liu L, Tiburtini M, Peruzzi L (2020) Chromosome numbers for the Italian flora: 9. Italian Botanist 9: 101-110. https://doi.org/10.3897/italianbotanist.9.54973

Figure 8 Potentilla detommasii Ten. from Belvedere del Malvento (Viggianello, Potenza), 2n = 14. Scale bar: 10 μm.

opencc-zeroJul 2020View details →

Data from: Snakeskin gourami (Trichopodus pectoralis) exhibits XX/XY sex determination and putative young Y chromosome shares sex chromosomal linkage homologies with those of amniotes

Snakeskin gourami (Trichopodus pectoralis) is one of the most common air-breathing freshwater fish of the Indochina peninsula. It has a high meat yield and is one of the top five aquaculture freshwater fish in Thailand. However, it takes 2–3 years for adults to reach sexual maturity. Snakeskin gourami is not externally sexually dimorphic and its sex determination remains unknown, complicating many aspects of broodstock management including sex manipulation. Understanding the sex determination system will contribute significantly towards full-scale commercialization. By characterizing the sex determination system in snakeskin gourami using cytogenetic approaches and Diversity Arrays Technology, we identified sex-specific loci in 16 phenotypic sex assignments of snakeskin gourami. Of the 39 loci present in all males, 4 male-linked loci reached the criteria of moderately sex-linked loci (70:30; males:females and 80:20; males:females). By contrast, only one female-linked locus was detected from moderately sex-linked loci. This suggests that snakeskin gourami exhibits an XX/XY sex determination mode. No different chromosomal patterns were observed in karyotype, C-banding, and microsatellite repeat fluorescence in situ hybridization mapping between males and females, and no male-specific loci of 100:0 (males:females) were observed in snakeskin gourami. This suggests that the putative Y chromosome is young and the non-recombination region is very cryptic. A total of 10.26% male-linked loci were involved with the sex developmental pathway in vertebrates and 5.13% showed partial homology with several amniote sex chromosomal linkages. Surprisingly, the hypothesis of an ancestral amniote super-sex chromosome with overlaps of partial sex chromosomal linkages was also found in teleosts. This approach provides a solid baseline to reveal the sex determination mechanism and identify potential sex determination regions in teleosts, allowing further investigation of genetic improvements in snakeskin gourami.

Data from: Chromosome-level genome assembly of the coastal horseshoe crab (Tachypleus gigas)

Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability of genomic resources for these species will be valuable in planning appropriate conservation measures. Whole-genome sequences are currently available for three species. In this study, we have generated a chromosome‐level genome assembly of the fourth species, the Asian coastal horseshoe crab Tachypleus gigas (genome size 2.0 Gb). The genome assembly has a scaffold N50 value of 140 Mb with approximately 97% of the assembly mapped to 14 scaffolds representing 14 chromosomes of T. gigas. In addition, we have generated the complete mitochondrial genome sequence and deep-coverage transcriptome assemblies for four tissues. A total of 26,159 protein-coding genes were predicted in the genome. The T. gigas genome contains five Hox clusters similar to the mangrove horseshoe crab Carcinoscorpius rotundicauda, suggesting that the common ancestor of horseshoe crabs already possessed five Hox clusters. Phylogenomic and divergence time analysis suggested that the American and Asian horseshoe crab lineages shared a common ancestor around the Silurian period (~436 Ma). Comparison of the T. gigas genome with those of other horseshoe crab species with chromosome-level assemblies provided insights into the chromosomal rearrangement events that occurred during the emergence of these species. The genomic resources of T. gigas will be useful for understanding their genetic diversity and population structure and would help in designing strategies for managing and conserving their stocks across Asia.

Genetic architecture of individual variation in recombination rate on the X-chromosome in cattle

Meiotic recombination is an essential biological process that ensures proper chromosome segregation and creates genetic diversity. Individual variation in global recombination rates has been shown to be heritable in several species and variants significantly associated with this trait have been identified. Recombination on the sex chromosome has often been ignored in these studies although this trait may be particularly interesting as it may correspond to a biological process distinct from that on autosomes. For instance, recombination in males is restricted to the pseudo-autosomal region (PAR). We herein used a large cattle pedigree with more than 100,000 genotyped animals to improve the genetic map of the X-chromosome and to study the genetic architecture of individual variation in recombination rate on the sex-chromosome (XRR). The length of the genetic map was 46.4 and 121.2 cM in males and females, respectively, but the recombination rate in the PAR was 6 times higher in males. The heritability of CO counts on the X-chromosome was comparable to that of autosomes in males (0.011) but larger than that of autosomes in females (0.024). XRR was highly correlated (0.76) with global recombination rate (GRR) in females, suggesting that both traits might be governed by shared variants. In agreement, a set of eleven previously identified variants associated with GRR had correlated effects on female XRR (0.86). In males, XRR and GRR appeared to be distinct traits, although more accurate CO counts on the PAR would be valuable to confirm these results.

Chromosome-level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)

Bivalves, a highly diverse and the most evolutionarily successful class of invertebrates native to aquatic habitats, provide valuable molecular resources for understanding the evolutionary adaptation and aquatic ecology. Here we reported a high-quality chromosome-level genome assembly of the razor clam Sinonovacula constricta using Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads and Hi-C reads. The genome size was 1,220.85 Mb, containing scaffold N50 of 65.93 Mb and contig N50 of 976.94 Kb. A total of 899 complete (91.92%) and seven partial (0.72%) matches of the 978 metazoa Benchmarking Universal Single-Copy Orthologs were determined in this genome assembly. And Hi-C scaffolding of the genome resulted in 19 pseudochromosomes. A total of 28,594 protein-coding genes were predicted in the S. constricta genome, of which 25,413 genes (88.88%) were functionally annotated. In addition, 39.79% of the assembled genome was composed of repetitive sequences, and 4,372 non-coding RNAs were identified. The enrichment analyses of the significantly expanded and contracted genes suggested an evolutionary adaptation of S. constricta to highly stressful living environments. In summary, the genomic resources generated in this work not only provide a valuable reference genome for investigating the molecular mechanisms of S. constricta biological functions and evolutionary.

Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes

Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The Siamese cobra (Naja kaouthia) exhibits ZZ/ZW heteromorphic sex chromosomes. The W sex chromosome contains a large number of repeats and shares several amniote sex chromosomal linkages. In conjunction with recent advances in high-throughput sequencing, Diversity Arrays Technology (DArTseq™) provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 perfectly sex-linked loci, 90 loci showed partial homology with several amniote sex chromosomal linkages, and 89 loci were homologous to transposable elements, which suggests that recombination suppression may be the crucial step in snake sex chromosome differentiation. Two loci were confirmed as W-specific nucleotides in females but not in males in the population examined by PCR amplification; one of the two loci (locus id: 100002617) was further amplified in females of the Indochinese spitting cobra (N. siamensis) but not in the other 22 snake species examined. Female-specific DArT markers were identified in Siamese cobra. These loci might result from a sex chromosome differentiation process between Z and W and involve putative sex-determination regions in Siamese cobra. Short sequences derived from DArTseq™ technology also shared linkage homologies among amniote sex chromosomes, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex chromosomal linkages. The locus (id: 100002617) shared in N. kaouthia and N. siamensis, but among 22 other snake species, indicates inheritance from a common ancestor as synapomorphic loci in the Naja lineage. The ease of use of the DArT markers and DArTseq™ platform provides a useful strategy for future research on sex chromosome evolution in snakes.