Reproduction is a fundamental aspect of life that affects all levels of biology, from genomes and development to population dynamics and diversification. The first Tree of Sex database synthesized a vast diversity of reproductive strategies and their intriguing distribution throughout eukaryotes. A decade on, we are reviving this initiative and greatly expanding its scope to provide the most comprehensive integration of knowledge on eukaryotic reproduction to date. In this perspective, we first identify important gaps in our current knowledge of reproductive strategies across eukaryotes. We then highlight a selection of questions that will benefit most from this new Tree of Sex project, including those related to the evolution of sex, modes of sex determination, sex chromosomes, and the consequences of various reproductive strategies. Finally, we outline our vision for the new Tree of Sex database and the consortium that will create it (treeofsex.org). The new database will cover all Eukaryota and include a wide selection of biological traits. It will also incorporate genomic data types that were scarce or non-existent at the time of the first Tree of Sex initiative. The new database will be publicly accessible, stable, and self-sustaining, thus greatly improving the accessibility of reproductive knowledge to researchers across disciplines for years to come. Lastly, the consortium will persist after the database is created to serve as a collaborative framework for research, prioritizing ethical standards in the collection, use, and sharing of reproductive data. The new Tree of Sex consortium is open, and we encourage all who are interested in this topic to join us.

• Klíčová slova
• asexual reproduction, biodiversity, database, ontology, sex chromosomes, sex determination, sexual reproduction,
• MeSH
• biologická evoluce * MeSH
• Eukaryota * fyziologie   genetika   MeSH
• procesy určující pohlaví MeSH
• rozmnožování * genetika   MeSH
• Publikační typ
• časopisecké články MeSH

For a long time, snakes were presented as a textbook example of a group with gradual differentiation of homologous ZZ/ZW sex chromosomes. However, recent advances revealed that the ZZ/ZW sex chromosomes characterize only caenophidian snakes and certain species of boas and pythons have nonhomologous XX/XY sex chromosomes. We used genome coverage analysis in four non-caenophidian species to identify their sex chromosomes, and we examined the homology of sex chromosomes across phylogenetically informative snake lineages. We identified sex chromosomes for the first time in 13 species of non-caenophidian snakes, providing much deeper insights into the evolutionary history of snake sex chromosomes. The evolution of sex chromosomes in snakes is more complex than previously thought. Snakes may have had ancestral XX/XY sex chromosomes, which are still present in a blind snake and some boas, and there were several transitions to derived XX/XY sex chromosomes with different gene content and two or even three transitions to ZZ/ZW sex chromosomes. However, we discuss more alternative scenarios. In any case, we document that (1) some genomic regions were likely repeatedly co-opted as sex chromosomes in phylogenetically distant lineages, even with opposite types of heterogamety; (2) snake lineages differ greatly in the rate of differentiation of sex chromosomes; (3) snakes likely originally possessed sex chromosomes prone to turnovers. The sex chromosomes became evolutionarily highly stable once their differentiation progressed in the megadiverse caenophidian snakes. Snakes thus provide an ideal system for studying the evolutionary factors that drive unequal rates of differentiation, turnovers and stability of sex chromosomes.

• Klíčová slova
• DNA-seq, genomics, qPCR, reptiles, sex chromosomes, sex determination,
• MeSH
• biologická evoluce MeSH
• fylogeneze MeSH
• hadi * genetika   MeSH
• molekulární evoluce MeSH
• pohlavní chromozomy * genetika   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

INTRODUCTION: Sex is a fundamental characteristic of an individual. It is therefore puzzling why in some systems sex is precisely determined by a genotype, while in others it is influenced by the environment or even subtle, not to say random, factors. Some stochasticity in sex determination would be expected if environmental conditions did not have a large sex-specific effect on fitness. Although data are only available for a small fraction of species, geckos show exceptional variability in sex determination. METHODS: We tested the effects of three incubation temperatures on sex ratio and adult body size in the invasive gecko Phelsuma laticauda and the vulnerable gecko Phelsuma nigristriata. RESULTS: We document temperature-dependent sex determination (TSD) in both species. Only females hatched at a low temperature (24°C), whereas male production peaked at an intermediate temperature (28°C) and declined, at least in P. laticauda, again at the highest temperature (31°C). Interestingly, full siblings hatched from eggs glued together during the incubation at temperatures producing both sexes are often of the opposite sex. We found no significant effect of incubation temperature on adult body length. CONCLUSIONS: Documentation of TSD in the day geckos has implications for conservation practice in environmental management of endangered species or eradication of invasive species. However, it appears that a very subtle (random?) factor may also be involved in their sex determination. In line with this, we found no significant effect of incubation temperature on adult body length.

• Klíčová slova
• Environmental sex determination, Invasive species, Reptiles, Temperature,
• MeSH
• ještěři * fyziologie   genetika   MeSH
• ohrožené druhy * MeSH
• poměr pohlaví MeSH
• procesy určující pohlaví * MeSH
• teplota MeSH
• velikost těla MeSH
• zavlečené druhy MeSH
• životní prostředí * MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Chameleons are well-known lizards with unique morphology and physiology, but their sex determination has remained poorly studied. Madagascan chameleons of the genus Furcifer have cytogenetically distinct Z and W sex chromosomes and occasionally Z1Z1Z2Z2/Z1Z2W multiple neo-sex chromosomes. To identify the gene content of their sex chromosomes, we microdissected and sequenced the sex chromosomes of F. oustaleti (ZZ/ZW) and F. pardalis (Z1Z1Z2Z2/Z1Z2W). In addition, we sequenced the genomes of a male and a female of F. lateralis (ZZ/ZW) and F. pardalis and performed a comparative coverage analysis between the sexes. Despite the notable heteromorphy and distinctiveness in heterochromatin content, the Z and W sex chromosomes share approximately 90% of their gene content. This finding demonstrates poor correlation of the degree of differentiation of sex chromosomes at the cytogenetic and gene level. The test of homology based on the comparison of gene copy number variation revealed that female heterogamety with differentiated sex chromosomes remained stable in the genus Furcifer for at least 20 million years. These chameleons co-opted for the role of sex chromosomes the same genomic region as viviparous mammals, lacertids and geckos of the genus Paroedura, which makes these groups excellent model for studies of convergent and divergent evolution of sex chromosomes.

• Klíčová slova
• Chameleons, Homology, Karyotypes, Microdissection, Sex chromosomes, qPCR,
• MeSH
• ještěři * genetika   MeSH
• molekulární evoluce MeSH
• pohlavní chromozomy genetika   MeSH
• procesy určující pohlaví genetika   MeSH
• savci genetika   MeSH
• sekvence nukleotidů MeSH
• variabilita počtu kopií segmentů DNA * MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Geckos are an excellent group to study the evolution of sex determination, as they possess a remarkable variability ranging from a complete absence of sex chromosomes to highly differentiated sex chromosomes. We explored sex determination in the Madagascar leaf-tail geckos of the genus Uroplatus. The cytogenetic analyses revealed highly heterochromatic W chromosomes in all three examined species (Uroplatus henkeli, U. alluaudi, U. sikorae). The comparative gene coverage analysis between sexes in U. henkeli uncovered an extensive Z-specific region, with a gene content shared with the chicken chromosomes 8, 20, 26 and 28. The genomic region homologous to chicken chromosome 28 has been independently co-opted for the role of sex chromosomes in several vertebrate lineages, including monitors, beaded lizards and monotremes, perhaps because it contains the amh gene, whose homologs were repeatedly recruited as a sex-determining locus. We demonstrate that all tested species of leaf-tail geckos share homologous sex chromosomes despite the differences in shape and size of their W chromosomes, which are not homologous to the sex chromosomes of other closely related genera. The rather old (at least 40 million years), highly differentiated sex chromosomes of Uroplatus geckos can serve as a great system to study the convergence of sex chromosomes evolved from the same genomic region.

• Klíčová slova
• DNA-seq, cytogenetics, evolution, genomics, qPCR, reptiles, sex chromosomes, sex determination,
• MeSH
• fylogeneze MeSH
• ještěři * genetika   MeSH
• pohlavní chromozomy genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Madagaskar MeSH

Scincoidea, the reptilian clade that includes girdled lizards, night lizards, plated lizards and skinks, are considered as a lineage with diversity in sex-determining systems. Recently, the hypothesis on the variability in sex determination in skinks and even more the absence of sex chromosomes in some of them has been rivalling. Homologous, evolutionary stable XX/XY sex chromosomes were documented to be widespread across skinks. However, sex determination in the other scincoidean families is highly understudied. ZZ/ZW sex chromosomes have been identified only in night lizards and a single species of plated lizards. It seems that although there are different sex chromosome systems among scincoidean lineages, they share one common trait: they are mostly poorly differentiated and often undetectable by cytogenetic methods. Here, we report one of the exceptions, demonstrating for the first time ZZ/ZW sex chromosomes in the plated lizard Zonosaurus madagascariensis. Its sex chromosomes are morphologically similar, but the W is clearly detectable by comparative genomic hybridization (CGH), suggesting that the Z and W chromosomes highly differ in sequence content. Our findings confirm the presence of female heterogamety in plated lizards and provides novel insights to expand our understanding of sex chromosome evolution in scincoidean lizards.

• Klíčová slova
• C-banding, CGH, FISH, ZZ/ZW, cytogenetics, karyotype, rDNA loci, sex chromosomes, sex determination, telomeres,
• MeSH
• ještěři * genetika   MeSH
• lidé MeSH
• pohlavní chromozomy genetika   MeSH
• procesy určující pohlaví * genetika   MeSH
• srovnávací genomová hybridizace MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Madagaskar MeSH

Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue of Phil. Trans. R. Soc. B. We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.

• Klíčová slova
• evolution, sex chromosomes, sex determination, vertebrates,
• MeSH
• biologická evoluce * MeSH
• obratlovci genetika   růst a vývoj   MeSH
• pohlavní chromozomy genetika   MeSH
• procesy určující pohlaví * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

This preface introduces the two parts of a theme issue on vertebrate sex chromosome evolution (title below). We invited and edited 22 articles concerning the following main topics (Part 1): sex determination without sex chromosomes and/or governed by epigenetics; origin of sex-determining genes; reasons for differentiation of sex chromosomes and differences in their rates of differentiation as well as (Part 2): co-option of the same linkage groups into sex chromosomes; is differentiation of sex chromosomes a unidirectional pathway?; consequences of differentiated sex chromosomes; differences in differentiation of sex chromosomes under male versus female heterogamety; evolution of sex chromosomes under hybridization and polyploidy. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.

• Klíčová slova
• evolution, sex chromosomes, vertebrates,
• MeSH
• molekulární evoluce * MeSH
• obratlovci genetika   MeSH
• pohlavní chromozomy genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• úvodní články MeSH

Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.

• Klíčová slova
• evolution, genomics, reproduction, sex chromosomes, sex determination, vertebrates,
• MeSH
• biologická evoluce * MeSH
• délka genomu * MeSH
• molekulární evoluce MeSH
• obratlovci genetika   MeSH
• ovarium růst a vývoj   MeSH
• pohlavní chromozomy genetika   MeSH
• procesy určující pohlaví * MeSH
• sexuální diferenciace genetika   MeSH
• testis růst a vývoj   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH

Amniotes possess astonishing variability in sex determination ranging from environmental sex determination (ESD) to genotypic sex determination (GSD) with highly differentiated sex chromosomes. Geckos are one of the few amniote groups with substantial variability in sex determination. What makes them special in this respect? We hypothesized that the extraordinary variability of sex determination in geckos can be explained by two alternatives: 1) unusual lability of sex determination, predicting that the current GSD systems were recently formed and are prone to turnovers; and 2) independent transitions from the ancestral ESD to later stable GSD, which assumes that geckos possessed ancestrally ESD, but once sex chromosomes emerged, they remain stable in the long term. Here, based on genomic data, we document that the differentiated ZZ/ZW sex chromosomes evolved within carphodactylid geckos independently from other gekkotan lineages and remained stable in the genera Nephrurus, Underwoodisaurus, and Saltuarius for at least 15 Myr and potentially up to 45 Myr. These results together with evidence for the stability of sex chromosomes in other gekkotan lineages support more our second hypothesis suggesting that geckos do not dramatically differ from the evolutionary transitions in sex determination observed in the majority of the amniote lineages.

• Klíčová slova
• DNA-seq, genomics, qPCR, reptiles, sex chromosomes, sex determination,
• MeSH
• biologická evoluce MeSH
• fylogeneze MeSH
• ještěři * genetika   MeSH
• pohlavní chromozomy genetika   MeSH
• procesy určující pohlaví genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH