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Early Cretaceous greenhouse pumped higher taxa diversification in spiders
Abstract
The Cretaceous experienced one of the most remarkable greenhouse periods in geological history. During this time, ecosystem reorganizations significantly impacted the diversification of many groups of organisms. The rise of angiosperms marked a major biome turnover. Notwithstanding, relatively little remains known about how the Cretaceous global ecosystem impacted the evolution of spiders, which constitute one of the most abundant groups of predators. Herein, we evaluate the transcriptomes of 91 taxa representing more than half of the spider families. We add 23 newly sequenced taxa to the existing database to obtain a robust phylogenomic assessment. Phylogenetic reconstructions using different datasets and methods obtain novel placements of some groups, especially in the Synspermiata and the group having a retrolateral tibial apophysis (RTA). Molecular analyses indicate an expansion of the RTA clade at the Early Cretaceous with a hunting predatory strategy shift. Fossil analyses show a 7-fold increase of diversification rate at the same period, but this likely owes to the first occurrences spider in amber deposits. Additional analyses of fossil abundance show an accumulation of spider lineages in the Early Cretaceous. We speculate that the establishment of a warm greenhouse climate pumped the diversification of spiders, in particular among webless forms tracking the abundance of insect prey. Our study offers a new pathway for future investigations of spider phylogeny and diversification.
... The ultra-conserved sequences for this study were obtained from the following sources: (1) published UCE studies: Starrett et al. (2017), Wood et al. (2018), , Kulkarni et al. (2020), , Maddison et al. (2020), Azevedo et al. (2022); (2) transcriptome based studies: Sharma et al. (2014), Zhao et al. (2014), Fernández et al. (2014Fernández et al. ( , 2018, Rix et al. (2018), Kallal et al. (2018), Shao & Li (2018), Kallal et al. (2020); (3) We analyzed 554 terminals of UCE data, representing 125 out of 132 (94.6% sampling) spider families (World Spider Catalog, 2022). The phylogenetic trees were rooted at the node containing the Xiphosura representatives, Tachypleus tridentatus and Limulus polyphemus. ...
... These araneoid triplet spigots may be reduced in some spiders such as Cepheia longiseta (Simon, 1881) (Synaphridae) (Lopardo & Hormiga, 2008) or absent (Mimetidae) . All genome-scale based phylogenies recover Theridiidae as a sister group of a lineage that includes all remaining araneoid families (Garrison et al., 2016;Fernández et al., 2018;Shao & Li, 2018;Kulkarni et al., 2020 (Figure 4). The transcriptome-based phylogeny of Fernández et al., (2018) placed Theridiidae as the sister group of Anapidae. ...
... Wheeler et al., (2017) point out that this grouping may be imposed by the constraints of the backbone transcriptomic phylogeny of Garrison et al., (2016) that they used. However, multiple transcriptomic phylogenies (Fernández et al., 2018;Shao & Li, 2018; and various other genomic data classes (UCEs, transcriptomes as nucleotides, amino acids) have placed Homalonychidae as sister group to the Oval calamistrum + Dionycha Clade with high support (UB >95%). This suggests that Zodarioidea may need to be recircumscribed to only include Zodariidae + Penestomidae, however we do not formally make any nomenclatural changes in this study. ...
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field as studying morphological characters; a few genetic markers have given way to genomic data sets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the interrelationships of several groups have now been studied using genomic data. About 50,500 extant spider species have been described so far, all with a conservative body plan, but innumerable morphological and behavioral peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the Spider Tree of Life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the currently known 132 (99%) spider families. To achieve this sampling, we combined a legacy data set of six Sanger-based markers with newly generated and publicly available genome-scale data sets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea, Synspermiata, etc.) are robust across different classes of data. However, several surprising new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits, and reproductive strategies.
... Recent phylogenomic analyses of spiders led to considerable changes in the taxonomic composition of haplogyne araneomorphs. Currently, haplogynes consist of the clade Synspermiata (18 families) and a clade formed by the families Hypochilidae and Filistatidae [10][11][12] (Fig. 1). These two clades currently include more than 6000 described species (based on the data of [13]). ...
... The Y chromosome was the smallest element of the karyotype Fig. 1 Phylogeny of spiders, with specific consideration on haplogyne spiders. The phylogenetic tree was constructed following [10] except for Telemidae [11]. Caponioidea: Caponiidae, Trogloraptoridae; Dysderoidea: Dysderidae, Oonopidae, Orsolobidae, Segestriidae; Scytodoidea: Drymusidae, Ochyroceratidae, Periegopidae, Psilodercidae, Scytodidae, Sicariidae Ávila Herrera et al. ...
... Chromosomes metacentric except for five submetacentric (nos. 2,8,[10][11][12], one subtelocentric (no. 13), and one acrocentric element (no. ...
Background:Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneo-morphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown.Results:Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X1X20, X1X2X30, X1X2Y, and X1X2X3X4Y ). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes.Conclusions:The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome–autosome and autosome–sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X1X2Y system is probably ancestral for haplogynes. Chromosomes of the X1X2Y system differ considerably in their pattern of evolution. In some pholcid clades, the X1X2Y system has transformed into the X1X20 or XY systems, and subsequently into the X0 system. The X1X2X30 system of Smeringopus pallidus probably arose from the X1X20 system by an X chromosome fission. The X1X2X3X4Y system of Kambiwa probably evolved from the X1X2Y system by integration of a chromosome pair.
... Recent phylogenomic analyses of spiders led to considerable changes in the taxonomic composition of haplogyne araneomorphs. Currently, haplogynes consist of the clade Synspermiata (18 families) and a clade formed by the families Hypochilidae and Filistatidae [10][11][12] (Fig. 1). These two clades currently include more than 6000 described species (based on the data of [13]). ...
... The Y chromosome was the smallest element of the karyotype Fig. 1 Phylogeny of spiders, with specific consideration on haplogyne spiders. The phylogenetic tree was constructed following [10] except for Telemidae [11]. Caponioidea: Caponiidae, Trogloraptoridae; Dysderoidea: Dysderidae, Oonopidae, Orsolobidae, Segestriidae; Scytodoidea: Drymusidae, Ochyroceratidae, Periegopidae, Psilodercidae, Scytodidae, Sicariidae Ávila Herrera et al. ...
... Chromosomes metacentric except for five submetacentric (nos. 2,8,[10][11][12], one subtelocentric (no. 13), and one acrocentric element (no. ...
Background
Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown.
Results
Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X 1 X 2 0, X 1 X 2 X 3 0, X 1 X 2 Y, and X 1 X 2 X 3 X 4 Y). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes.
Conclusions
The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome–autosome and autosome–sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X 1 X 2 Y system is probably ancestral for haplogynes. Chromosomes of the X 1 X 2 Y system differ considerably in their pattern of evolution. In some pholcid clades, the X 1 X 2 Y system has transformed into the X 1 X 2 0 or XY systems, and subsequently into the X0 system. The X 1 X 2 X 3 0 system of Smeringopus pallidus probably arose from the X 1 X 2 0 system by an X chromosome fission. The X 1 X 2 X 3 X 4 Y system of Kambiwa probably evolved from the X 1 X 2 Y system by integration of a chromosome pair. Nucleolus organizer regions have frequently expanded on sex chromosomes, most probably by ectopic recombination. Our data suggest the involvement of sex chromosome-linked NORs in achiasmatic pairing.
... family-level) of analyses of spider interfamilial relationships have increased (e.g. Garrison et al., 2016;Cheng and Piel, 2018;Hedin et al., 2018;Kallal et al., 2018;Shao and Li, 2018;Wood et al., 2018;Fern andez et al., 2018a;Hedin et al., 2019;Kuntner et al., 2019;Michalik et al., 2019;Kulkarni et al., 2019;Opatova et al., 2020). The increasing consensus has led to more resolved and robust trees at various phylogenetic scales, making comparative questions interpretable in new ways. ...
... Voucher specimens and tissue for these animals are deposited at the Museum of Comparative Zoology at Harvard University. In addition to material sequenced previously (Bond et al., 2014;Fern andez et al., 2014;French et al., 2014;Sanggaard et al., 2014;Sharma et al., 2014;Zhao et al., 2014;Brewer et al., 2015;Hedin, 2015;Meng et al., 2015;Garrison et al., 2016;Rix et al., 2017;Cheng and Piel, 2018;Kallal et al., 2018;Shao and Li, 2018;Fern andez et al., 2018a;Michalik et al., 2019), our available taxon sampling includes 272 terminals, of which 263 are spiders (Table S01 in Appendix S1). This sums to >100 additional taxa in comparison to the largest published dataset (Fern andez et al., 2018a). ...
... Our study, with strategically increased taxon sampling to maximize web diversity across lineages and a variety of analytical methods produced a well-resolved spider tree-of-life. For the overlapping taxa, results recovered most of the phylogenetic relationships established by previous works (Garrison et al., 2016;Dimitrov et al., 2017;Wheeler et al., 2017;Cheng and Piel, 2018;Kallal et al., 2018;Shao and Li, 2018;Fern andez et al., 2018a;Hedin et al., 2019;Kulkarni et al., 2019;Michalik et al., 2019;Kulkarni et al., 2020), reinforcing several previous topologies. For this reason, we limit our discussion of relationships to highlight areas in which our results are novel. ...
High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long‐standing hypotheses. Likewise, the evolution of spider webs—perhaps their most emblematic attribute—is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages using a variety of orthology assessment methods, occupancy thresholds, tree inference methods and support metrics. Our analyses include families not previously sampled in transcriptomic analyses, such as Symphytognathidae, the only araneoid family absent in such prior works. We find support for the major established spider lineages, including Mygalomorphae, Araneomorphae, Synspermiata, Palpimanoidea, Araneoidea and the Retrolateral Tibial Apophysis Clade, as well as the uloborids, deinopids, oecobiids and hersiliids Grade. Resulting trees are evaluated using bootstrapping, Shimodaira–Hasegawa approximate likelihood ratio test, local posterior probabilities and concordance factors. Using structured Markov models to assess the evolution of spider webs while accounting for hierarchically nested traits, we find multiple convergent occurrences of the orb web across the spider tree‐of‐life. Overall, we provide the most comprehensive spider tree‐of‐life to date using transcriptomic data and use new methods to explore controversial issues of web evolution, including the origins and multiple losses of the orb web.
... With more than 48,500 described species (147), spiders (Araneae) make up one of the most diverse animal lineages. Their high species diversity coupled with a conservative body plan and generalist predatory habits have attracted the attention of comparative biologists seeking to understand spider diversification (e.g., 55,57,122). All spiders produce silk and use several different types of silk in a variety of ways (135,136). ...
... The advent of genomic-scale sequencing and new comparative methods have allowed phylogenetic analyses of hundreds of species, resulting in numerous studies aiming to understand spider diversification in a quantitative framework with an explicit and empirical temporal scale (e.g., 17,19,44,50,55,122). Several recent studies have challenged some of the traditional hypotheses about spider diversification, highlighting the importance of environmental factors such as habitat heterogeneity and climate or behavior (e.g., 44,50,55,92,122,136), while others have argued for renewed support of some of the classical hypotheses, such as those that link spider diversification to that of their insect prey. ...
... The advent of genomic-scale sequencing and new comparative methods have allowed phylogenetic analyses of hundreds of species, resulting in numerous studies aiming to understand spider diversification in a quantitative framework with an explicit and empirical temporal scale (e.g., 17,19,44,50,55,122). Several recent studies have challenged some of the traditional hypotheses about spider diversification, highlighting the importance of environmental factors such as habitat heterogeneity and climate or behavior (e.g., 44,50,55,92,122,136), while others have argued for renewed support of some of the classical hypotheses, such as those that link spider diversification to that of their insect prey. For example, the diversity and abundance of theridiids (cob web spiders) has been attributed to the diversification of ants (84), and the higher diversification rates in the retrolateral tibial apophysis (RTA) clade, a diverse lineage of mainly cursorial (wandering hunting) spiders that includes wolf and jumping spiders, has been explained as a result of a transition from foraging with webs to cursorial habits (57). ...
Spiders (Araneae) make up a remarkably diverse lineage of predators that have successfully colonized most terrestrial ecosystems. All spiders produce silk, and many species use it to build capture webs with an extraordinary diversity of forms. Spider diversity is distributed in a highly uneven fashion across lineages. This strong imbalance in species richness has led to several causal hypotheses, such as codiversification with insects, key innovations in silk structure and web architecture, and loss of foraging webs. Recent advances in spider phylogenetics have allowed testing some of these hypotheses, but results are often contradictory, highlighting the need to consider additional drivers of spider diversification. The spatial and historical patterns of diversity and diversification remain contentious. Comparative analyses of spider diversification will advance only if we continue to make progress with studies of species diversity, distribution, and phenotypic traits, together with finer-scale phylogenies and genomic data.
Expected final online publication date for the Annual Review of Entomology, Volume 66 is January 11, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
... Wood et al., 2013;Appelhans et al., 2018;Chousou-Polydouri et al., 2019;Wang et al., 2019), identifying drivers of lineage diversification (e.g. Désamoré et al., 2018;Fernández et al., 2018;Shao & Li, 2018;Flores-Abreu et al., 2019), or understanding the tempo of morphological evolution (e.g. Hodgson et al., 2009;Wood, 2017;Rolland et al., 2018;Ceccarelli et al., 2019). ...
... The advent of phylogenomics allowed for the collection of massive amounts of data and helped solving many contentious nodes of the spider tree of life while providing further evidence for long-recognized clades (e.g. Bond et al., 2014;Garrison et al., 2016;Fernández et al., 2018;Shao & Li, 2018). The advent of sequence-based systematics and relaxed molecular clock methods led to an abrupt increase in studies using fossil calibrations to generate dated trees, with no less than 44 articles using these methods published since 2007 (see Table 1). ...
... Finally, we calculated the minimum changes in taxic diversity using spider lineages with rank of family or above as proxies (as in Penney et al., 2003, following Smith, 1994. For this, we built a composite family-level phylogeny for spiders based on recent hypotheses: we used the tree from Wheeler et al. (2017) as a basis, with modifications of the positions of particular groups based on more recent results [Leptonetidae, Austrochiloidea, Palpimanoidea, and Araneoidea, among others (Fernández et al., 2018); Telemidae (Shao & Li, 2018); Trogloraptoridae (Michalik et al., in press)]. Based on this composite tree, we plotted the known stratigraphic range of each family based on our review using the functions timePaleoPhy and geoscalePhylo in the paleotree and strap packages, respectively (Bapst, 2012;Bell & Lloyd, 2015). ...
Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long‐standing debate in spider evolution – we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous–Paleogene (K–Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA‐clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA‐clade spiders.
... tepidariorum), and Matthias Pechmann (A. geniculata). Topology and branch lengths based on divergence time estimates from Shao and Li (2018). ...
... Despite the loss of the AMEs exhibited in S. senoculata likely occurring at the base of Dysderoidea, some 100-150 Ma (Shao and Li 2018), we detected early activation of the RDGs otd, eya, and so in the principal eye primordia up to stage 10/11. This is reminiscent of early eye development in eyeless subterranean species such as Astyanax mexicanus, wherein the eyes develop to a relatively advanced stage before apoptotic events in the lens trigger their arrest and degradation (see Jeffery 2009; Rétaux and Casane 2013; Wilkens and Strecker 2017 for reviews). ...
Visual systems provide a key interface between organisms and their surroundings, and have evolved in many forms to perform diverse functions across the animal kingdom. Spiders exhibit a range of visual abilities and ecologies, the diversity of which is underpinned by a highly versatile, modular visual system architecture. This typically includes eight eyes of two developmentally distinct types, but the number, size, location, and function of the eyes can vary dramatically between lineages. Previous studies of visual system development in spiders have confirmed that many components of the retinal determination gene (RDG) network are conserved in common with other arthropods, but so far, comparative studies among spiders are lacking. We characterised visual system development in eight species of spiders representing a range of morphologies, visual ecologies, and phylogenetic positions, to determine how these diverse configurations are formed, and how they might evolve. Combining synchrotron radiation tomography, transcriptomics, in situ hybridisation, and selection analyses, we describe the repertoires and expression of key RDGs in relation to adult morphology, and identify key molecular players, timepoints, and developmental events that may contribute to adult diversity. In particular, we discuss the molecular and developmental underpinnings of eye size, number, position, and identity across spiders, and highlight key areas for further functional analyses.
... As an ancient group, spiders can be dated back to the Devonian (>380 Ma), and have adapted to diverse ecosystems with remarkable behaviour and morphology during their evolutionary history. Over the years, arachnologists have worked long and hard to understand the diversification and evolutionary history of spiders (Garrison et al., 2016;Fern andez et al., 2018;Shao and Li, 2018;Dimitrov and Hormiga, 2020). ...
... This spider lineage is extremely diverse with over 25 000 described species (Dimitrov and Hormiga, 2020;World Spider Catalog, 2022), including the most species-rich spider family Salticidae (>6000 described species; World Spider Catalog, 2022), which are well known for their acute vision and spectacular courtship dances as well as the recently discovered milk provision (Richman and Jackson, 1992;Foelix, 1996;Chen et al., 2018). Recent divergence dating analyses suggested that the RTA clade is relatively young (139-161 Ma) compared with the Araneoidea clade of largely orb-weaving spiders, but the main drivers for its diversification remain contentious (Garrison et al., 2016;Fern andez et al., 2018;Shao and Li, 2018;Dimitrov and Hormiga, 2020;Magalhaes et al., 2020). In order to better understand the evolution of this major clade of spiders, we need to build on recent work (Miller et al., 2010;Agnarsson et al., 2013;Maddison, 2015;Wheeler et al., 2017;Azevedo et al., 2022) to resolve its phylogeny more fully and with better support. ...
Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.
... Extinct spider taxa have usually been used for anchoring the age of particular nodes in the phylogenetic trees depicting relationships among extant taxa (e.g. Dimitrov et al., 2013;Benavides et al., 2017;Fernández et al., 2018;Li & Li, 2018;Shao & Li, 2018;Magalhaes et al., 2020). By contrast, only several studies used fossil spiders as terminal taxa in the phylogenetic analysis (Wood et al., 2012(Wood et al., , 2013(Wood et al., , 2015Wood, 2017;Selden et al., 2020). ...
... Extinct spider taxa have usually been used for anchoring the age of particular nodes in the phylogenetic trees depicting relationships among extant taxa (e.g. Dimitrov et al., 2013;Benavides et al., 2017;Fernández et al., 2018;Li & Li, 2018;Shao & Li, 2018;Magalhaes et al., 2020). By contrast, only several studies used fossil spiders as terminal taxa in the phylogenetic analysis (Wood et al., 2012(Wood et al., , 2013(Wood et al., , 2015Wood, 2017;Selden et al., 2020). ...
New lagonomegopid spiders are described from Mid-Cretaceous Myanmar (Burmese) amber. Two new genera and species based on single specimens, Scopomegops fax gen. & sp. nov. and Hiatomegops spinalis gen. & sp. nov. are described. Two specimens belonging to Lineaburmops beigeli are further described. Additionally, after re-examining the holotype of Odontomegops titan, a detailed description of its basal ventral abdomen is added here. A phylogenetic analysis was performed to investigate the phylogenetic placement of Lagonomegopidae. A matrix of 79 morphological characters, scored for six lagonomegopid taxa and 26 non-lagonomegopid taxa, was analysed through parsimony and Bayesian phylogenetic inference. Our results recover extant Palpimanoidea as a monophyletic group and partly suggest that Lagonomegopidae is the sister-group to extant Palpimanoidea. The external sexual organs, retrolateral tibial apophysis on the male palp and tracheal spiracle in lagonomegopids are discussed.
... Purification of mRNA, library preparation, sequencing (Illumina HiSeq™ 2500) and quality control were done by Novogene Bioinformatics Technology Co. Next, clean reads were assembled using default parameters in Trinity v2.0.5 (Grabherr et al. 2011). Other detailed information and parameters followed Shao and Li (2018). All specimens used in this study were legally collected. ...
... There are several fossil Agelenidae but none within Pireneitega, so the divergence times of Pireneitega species were calibrated based on the latest reliable dating framework for spiders (Shao and Li 2018) and coelotines (Zhao and Li 2017). The size of the transcriptome dataset precluded the use of some computationally intensive dating methods, such as BEAST (Drummond and Rambaut 2007), so the package mcmctree in conjunction with baseml of PAML v4.8 (Yang 2007) was used to estimate node ages and reduced the computational load by approximating the likelihood. ...
The withdrawal of the Tethys Sea and the formation of the Alpine‐Himalayan orogenic belt profoundly impacted the distribution and composition of terrestrial biota in Eurasia. However, studies that have explicitly addressed the potential links between the series of tectonic activities in the Tethyan region and the formation of extratropical biodiversity hotspots in the Alpine‐Himalayan belt are rare. Spiders in the genus Pireneitega (Agelenidae) are found throughout Eurasia and show high species richness in these hotspots. Thus, Pireneitega spiders may serve as a model group to shed light on how past tectonic events shaped Eurasian hotspots. To reconstruct the spatial and temporal evolution of Pireneitega spp., we conducted an integrative historical biogeographical analysis using thousands of novel DNA sequences and five novel transcriptome sequences from different species. Species distribution modelling based on complete geographical distribution information was used to assess the ecological preferences and the potential ecological interchangeability of Pireneitega species. Our study suggests that the rapid expansion of Pireneitega in Eurasia benefitted from regression of the Tethys Sea in the early Oligocene. Most Pireneitega species are distributed allopatrically, but in similar niches. The diversification of Pireneitega species relied on invading numerous new isolated habitats created by the uplift of Alpine‐Himalayan mountains during the Miocene (wet valley model). These results imply that the formation of Alpine‐Himalayan hotspots was driven by the series of tectonic events in the Tethyan region during the Oligocene–Miocene.
... nov. We used two segestriid species as outgroups, as Segestriidae is considered the sister lineage of Telemidae (Shao and Li 2018). In total, 73 taxa were included in our molecular dataset. ...
... nov., P. nuocnutensisZhao & Li, 2018, P. spirulata Li, 2018, P. tham sp. nov., and P. zhenzhuang Zhao &Li, 2018 are not grouped and seem to represent groups of their own.Telema dengi Tong and Li 2008a: 69, figs 1C, 4A-H, 6 (♂♀); Tong 2013: 73, figs 31N, 88A-H (♂♀). Pinelema dengi comb. ...
This paper revised all known species of Telemidae (Arachnida, Araneae) in Asia, combined morphological characters and molecular phylogenetic analyses. Meanwhile, 4 new genera and 12 new species were decribed here. Furthermore, the genus Pinelema Wang & Li, 2020 is divided into seven species groups based on male morphological characters.
... nov. We used two segestriid species as outgroups, as Segestriidae is considered the sister lineage of Telemidae (Shao and Li 2018). In total, 73 taxa were included in our molecular dataset. ...
... nov., P. nuocnutensisZhao & Li, 2018, P. spirulata Li, 2018, P. tham sp. nov., and P. zhenzhuang Zhao &Li, 2018 are not grouped and seem to represent groups of their own.Telema dengi Tong and Li 2008a: 69, figs 1C, 4A-H, 6 (♂♀); Tong 2013: 73, figs 31N, 88A-H (♂♀). Pinelema dengi comb. ...
Species of the spider family Telemidae Fage, 1913 from East and Southeast Asia are revised. Four new genera are erected: Mekonglema Zhao & Li, gen. nov. with the type species Mekonglema bailang Zhao & Li, sp. nov. (♂♀, Yunnan, China), Siamlema Zhao & Li, gen. nov. with the type species Siamlema changhai Zhao & Li, sp. nov. (♂♀, southern Thailand), Sundalema Zhao & Li, gen. nov. with the type species Sundalema bonjol Zhao & Li, sp. nov. (♂♀, Sumatra), and Zhuanlema Zhao & Li, gen. nov. with the type species Zhuanlema peteri Zhao & Li, sp. nov. (♂♀, northern Laos). Eight additional new species
are described: Mekonglema kaorao Zhao & Li, sp. nov. (♂♀, northern Laos), M. walayaku Zhao & Li, sp. nov. (♂♀, Yunnan, China), M. yan Zhao & Li, sp. nov. (♂♀, Yunnan, China), Pinelema daguaiwan Zhao & Li, sp. nov. (♂♀, Guangxi, China), P. shiba Zhao & Li, sp. nov. (♂♀, Guangxi, China), P. tham Zhao & Li, sp. nov. (♂♀, northern Laos), Siamlema suea Zhao & Li, sp. nov. (♂♀, southern Thailand), and Sundalema khaorakkiat Zhao & Li, sp. nov. (♂♀, southern Thailand). Thirty species are transferred from the genus Telema Simon, 1882 to the genera Pinelema Wang & Li, 2012, Sundalema Zhao & Li, gen. nov., and Telemofila Wunderlich, 1995. Seychellia xinpingi Lin & Li, 2008 is transferred to Mekonglema gen. nov. as M. xinpingi comb. nov. Furthermore, the genus Pinelema is divided into seven species groups based on male morphological characters.
... We used two molecular data sets: one that emphasizes genomic coverage and another that emphasizes geographic coverage (the full data sets are provided in the Supplementary Tables S1 and S2 available on Dryad at https://doi.org/10.5061/dryad.kd2b16c). The transcriptomic data set consisted of six novel transcriptome sequences and 119 previously available transcriptomic data (Bond et al. 2014;Fernández et al. 2014;Garrison et al. 2016;Shao and Li 2018). New transcriptomic data were generated for six species representing one ochyroceratid taxon and five psilodercid taxa (Supplementary Table S2 available on Dryad). ...
... Purification of mRNA, library preparation, sequencing, and quality control were done by Novogene Bioinformatics Technology Co. Ltd. We used the method described in Shao and Li (2018) to generate orthologs. To minimize any negative effects of saturation, only the first and second positions of nucleotide data were used. ...
Biological migrations between India and Southeast (SE) Asia provide an ideal system for exploring the effects of geology and climate on species ranges. Geologists have confirmed that the direct collision between India and Eurasia occurred in the Early Eocene, but most migrations occurred between the Indian subcontinent and SE Asia rather than the former and the southern margin of Eurasia. To explain this seemingly paradoxical disconnect between the routes of plate movement and biological migration, we studied the evolutionary history of the tropical spider family Ochyroceratidae based on 101 globally distributed species. We infer a robust dated phylogeny using both transcriptomic data and a dataset of classical markers and relate these to biogeographic and climatic analyses. Our results indicate that the monophyly of Ochyroceratidae is strongly supported, and the divergence times suggest a Cretaceous Gondwanan origin of the family. Reconstructed biogeographic histories support a dispersal event from the Indian subcontinent to islands of SE Asia 55-38 million years ago. Climatic analyses and the fossil record reveal that ochyroceratids are characterized by a high degree of tropical niche conservatism, and that the ancestor of the Indian and SE Asian clades originated in very warm, wet environments. Early Eocene tropical, perhumid climates in India and SE Asia may have facilitated ochyroceratid migration, whereas the dry or seasonal climate extending from the eastern coast of China to Central Asia may have acted as a barrier, preventing dispersal. Our analyses suggest that climate plays a more important role than geology in biological migration from the Indian subcontinent to SE Asia, providing new insights into the Indian-Asian biogeographic link.
... S1 and S2, Supplementary Table 1). We complemented these new transcriptomes with six existing transcriptomes from closely related species 28,[33][34][35][36][37][38] (Supplementary Table 2). In addition, we included two available genomes of social spider species, Stegodyphus dumicola and Stegodyphus mimosarum. ...
The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.
... Haplogyne araneomorphs ("haplogynes") consist of the Synspermiata clade and two families, Filistatidae and Hypochilidae (Wheeler et al. 2017;Shao and Li 2018). Haplogynes currently include more than 6150 described species placed in 20 families (based on data of World Spider Catalog 2022). ...
Haplogyne araneomorphs are a diverse spider clade. Their karyotypes are usually predominated by biarmed (i.e., metacentric and submetacentric) chromosomes and have a specific sex chromosome system, X 1 X 2 Y. These features are probably ancestral for haplogynes. Nucleolus organizer regions (NORs) spread frequently from autosomes to sex chromosomes in these spiders. This study focuses on pholcids (Pholcidae), a highly diverse haplogyne family. Despite considerable recent progress in pholcid cytogenetics, knowledge on many clades remains insufficient including the most species-rich pholcid genus, Pholcus Walckenaer, 1805. To characterize the karyotype differentiation of Pholcus in Europe, we compared karyotypes, sex chromosomes, NORs, and male meiosis of seven species [ P. alticeps Spassky, 1932; P. creticus Senglet, 1971; P. dentatus Wunderlich, 1995; P. fuerteventurensis Wunderlich, 1992; P. phalangioides (Fuesslin, 1775); P. opilionoides (Schrank, 1781); P. silvai Wunderlich, 1995] representing the dominant species groups in this region. The species studied show several features ancestral for Pholcus , namely the 2n♂ = 25, the X 1 X 2 Y system, and a karyotype predominated by biarmed chromosomes. Most taxa have a large acrocentric NOR-bearing pair, which evolved from a biarmed pair by a pericentric inversion. In some lineages, the acrocentric pair reverted to biarmed. Closely related species often differ in the morphology of some chromosome pairs, probably resulting from pericentric inversions and/or translocations. Such rearrangements have been implicated in the formation of reproductive barriers. While the X 1 and Y chromosomes retain their ancestral metacentric morphology, the X 2 chromosome shows a derived (acrocentric or subtelocentric) morphology. Pairing of this element is usually modified during male meiosis. NOR patterns are very diverse. The ancestral karyotype of Pholcus contained five or six terminal NORs including three X chromosome-linked loci. The number of NORs has been frequently reduced during evolution. In the Macaronesian clade, there is only a single NOR-bearing pair. Sex chromosome-linked NORs are lost in Madeiran species and in P. creticus . Our study revealed two cytotypes in the synanthropic species P. phalangioides (Madeiran and Czech), which differ by their NOR pattern and chromosome morphology. In the Czech cytotype, the large acrocentric pair was transformed into a biarmed pair by pericentric inversion.
... Haplogyne araneomorphs ("haplogynes") consist of the Synspermiata clade and two families, Filistatidae and Hypochilidae (Wheeler et al. 2017;Shao and Li 2018). Haplogynes currently include more than 6150 described species placed in 20 families (based on data of World Spider Catalog 2022). ...
Haplogyne araneomorphs are a diverse spider clade. Their karyotypes are usually predominated by biarmed (i.e., metacentric and submetacentric) chromosomes and have a specific sex chromosome system, X 1 X 2 Y. These features are probably ancestral for haplogynes. Nucleolus organizer regions (NORs) spread frequently from autosomes to sex chromosomes in these spiders. This study focuses on pholcids (Pholcidae), a highly diverse haplogyne family. Despite considerable recent progress in pholcid cytogenetics, knowledge on many clades remains insufficient including the most species-rich pholcid genus, Pholcus Walckenaer, 1805. To characterize the karyotype differentiation of Pholcus in Europe, we compared karyotypes, sex chromosomes, NORs, and male meiosis of seven species [P. alticeps Spassky, 1932; P. creticus Senglet, 1971; P. dentatus Wunderlich, 1995; P. fuerteventurensis Wunderlich, 1992; P. phalangioides (Fuesslin, 1775); P. opilionoides (Schrank, 1781); P. silvai Wunderlich, 1995] representing the dominant species groups in this region. The species studied show several features ancestral for Pholcus, namely the 2n♂ = 25, the X 1 X 2 Y system, and a karyotype predominated by biarmed chromosomes. Most taxa have a large acro-centric NOR-bearing pair, which evolved from a biarmed pair by a pericentric inversion. In some lineages, * Those authors contributed equally to this work. A peer-reviewed open-access journal Jiří Král et al. / Comparative Cytogenetics 16(4): 185-209 (2022) 186 the acrocentric pair reverted to biarmed. Closely related species often differ in the morphology of some chromosome pairs, probably resulting from pericentric inversions and/or translocations. Such rearrangements have been implicated in the formation of reproductive barriers. While the X 1 and Y chromosomes retain their ancestral metacentric morphology, the X 2 chromosome shows a derived (acrocentric or sub-telocentric) morphology. Pairing of this element is usually modified during male meiosis. NOR patterns are very diverse. The ancestral karyotype of Pholcus contained five or six terminal NORs including three X chromosome-linked loci. The number of NORs has been frequently reduced during evolution. In the Macaronesian clade, there is only a single NOR-bearing pair. Sex chromosome-linked NORs are lost in Madeiran species and in P. creticus. Our study revealed two cytotypes in the synanthropic species P. phalan-gioides (Madeiran and Czech), which differ by their NOR pattern and chromosome morphology. In the Czech cytotype, the large acrocentric pair was transformed into a biarmed pair by pericentric inversion.
... A previous study showed that spiders could build better traps using their prey capture experience (Heiling and Herberstein,1999), implying that spiders' construction behaviors are not simply passive. Contrarily, web-building behaviors allow spiders to alter environmental states in various ways, allowing spiders to move away from substrate constraints and expand into various aerial habitats (sheltered and open) (nodes 5 and 7 in Fig. 3a), especially in different vegetation structures following the radiation of angiosperms (Shao and Li 2018;Benton et al. 2022). The exception is that the occurrence of suspending web-building behavior is likely to be a single origin and is consistent with the transfer of habitat to the sheltered ground habitat. ...
What happens when organisms actively modify their environment? Clarifying the role of construction behavior on a macroevolutionary scale is crucial to interpreting phenotypic evolution. Spiders, an extremely successful group of animals exhibiting a wide variety of functional, morphological, and behavioral diversity, are ideal candidates to test whether animal behaviors are related to their phenotypic evolution. Herein, we reconstructed the phylogenomic relationships of 303 spiders covering 105 families with 99 newly developed molecular markers that universally apply across Araneae, and explicitly tested the potential link between construction behavior and somatic evolution based on extensive morphological data from 3,342 extant species and 682 fossil species. Our dated molecular phylogeny provides the backbone for analyses, revealing the behavioral and ecological processes behind these spiders' morphological adaptations. Evolutionary model analyses showed the artifacts constructed by spiders, especially the suspending webs, expand the spider's ability to inhabit different habitats. These artifacts have more substantial impacts on their somatic traits than habitats and promote different trajectories of morphological evolution. Specifically, for spiders, silk-lined burrowing produced larger bodies, relatively shorter legs, and longer patellae, while web-building produced smaller bodies, relatively long legs, and shorter patellae, and hunting promoted an intermediate morphological size. Molecular convergence analysis showed that genes related to morphogenesis or response to stimulus and stress are enriched in spiders with construction behavior. Our study demonstrated that the construction behavior of an animal plays a crucial role in determining the direction and intensity of the selection pressure imposed on it and provides strong evidence that construction behaviors are associated with phenotypic evolution on macroevolutionary timescales.
... Most of the RTA clade are hunting predators and important natural enemies of many insect pests (e.g., wolf spiders, jumping spiders, running spiders, and crab spiders) (Garrison et al., 2016;Wheeler et al., 2017;Magalhaes et al., 2020). The RTA clade exhibits a worldwide distribution and is assumed to have emerged in the Jurassic period (139-161 million years ago (Ma)) (Garrison et al., 2016;Fernandez et al., 2018;Shao and Li, 2018;Magalhaes et al., 2020). According to male palp, trichobothria on the tarsi and metatarsi, the RTA clade is divided into four groups: Zodarioidea, Dionycha, Marronoid clade, and Oval calamistrum clade (Wheeler et al., 2017;Kallal et al., 2020). ...
The retrolateral tibial apophysis (RTA) clade is the largest spider lineage within Araneae. To better understand the diversity and evolution, we newly determined mitogenomes of ten RTA species from six families and performed a comparative mitogenomics analysis by combining them with 40 sequenced RTA mitogenomes available on GenBank. The ten mitogenomes encoded 37 typical mitochondrial genes and included a large non-coding region (putative control region). Nucleotide composition and codon usage were well conserved within the RTA clade, whereas diversity in sequence length and structural features was observed in control region. A reversal of strand asymmetry in nucleotide composition, i.e., negative AT-skews and positive GC-skews, was observed in each RTA species, likely resulting from mitochondrial gene rearrangements. All protein-coding genes were evolving under purifying selection, except for atp8 whose Ka/Ks was larger than 1, possibly due to positive selection or selection relaxation. Both mutation pressure and natural selection might contribute to codon usage bias of 13 protein-coding genes in the RTA lineage. Phylogenetic analyses based on mitogenomic data recovered a family-level phylogeny within the RTA; {[(Oval calamistrum clade, Dionycha), Marronoid clade], Sparassidae}. This study characterized RTA mitogenomes and provided some new insights into the phylogeny and evolution of the RTA clade.
... The second-largest clade of terrestrial animals (Table 1) includes spiders, scorpions and ticks (Stork, 2018). Spiders as predators on insects have often been cited as beneficiaries of the ATR, and this is supported by recent phylogenomic analyses (Garrison et al., 2016;Shao & Li, 2018): the hyperdiverse RTA spider clade, comprising 30 000 species of ground-dwelling, webless, hunting spiders, diversified 125-100 Ma in response to expansions of insect numbers, especially nonflying forms that lived in leaf litter and provided their food. The fossil record of spiders mainly comprises finds from sites of exceptional preservation, including ancient ambers, and these show that three modern families arose in the Triassic and Jurassic, 21 in the Cretaceous, and a further 40 in the Palaeogene (Selden & Penney, 2010). ...
Biodiversity today has the unusual property that 85% of plant and animal species live on land rather than in the sea, and half of these live in tropical rainforests. An explosive boost to terrestrial diversity occurred from c. 100–50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth‐life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species diversity of terrestrial environments. This boost in terrestrial biodiversity coincided with innovations in flowering plant biology and evolutionary ecology, including their flowers and efficiencies in reproduction; coevolution with animals, especially pollinators and herbivores; photosynthetic capacities; adaptability; and ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern biodiversity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.
... Using transcriptomes, Garrison et al. (2016) recovered leptonetids outside of Synspermiata, placing Calileptoneta Platnick, 1986 as sister to Entelegynae. Several studies built upon the foundation of Garrison et al. (2016), including Shao and Li (2018) who recovered leptonetines as sister to entelegynes but did not include austrochiloids as part of their study. Fernández et al. (2018) added transcriptomes for both leptonetid subfamilies (Archoleptoneta and Calileptoneta) and in their preferred topology recovered a monophyletic Leptonetidae sister to austrochiloids (Fig. 2). ...
Leptonetidae are rarely encountered spiders, usually associated with caves and mesic habitats, and are disjunctly distributed across the Holarctic. Data from ultraconserved elements (UCEs) were used in concatenated and coalescent-based analyses to estimate the phylogenetic history of the family. Our taxon sample included close outgroups, and 90% of described leptonetid genera, with denser sampling in North America and Mediterranean Europe. Two data matrices were assembled and analysed; the first ‘relaxed’ matrix includes the maximum number of loci and the second ‘strict’ matrix is limited to the same set of core orthologs but with flanking introns mostly removed. A molecular dating analysis incorporating fossil and geological calibration points was used to estimate divergence times, and dispersal–extinction–cladogenesis analysis (DEC) was used to infer ancestral distributions. Analysis of both data matrices using maximum likelihood and coalescent-based methods supports the monophyly of Archoleptonetinae and Leptonetinae. However, relationships among Archoleptonetinae, Leptonetinae, and Austrochiloidea are poorly supported and remain unresolved. Archoleptonetinae is elevated to family rank Archoleptonetidae (new rank) and Leptonetidae (new status) is restricted to include only members of the subfamily Leptonetinae; a taxonomic review with morphological diagnoses is provided for both families. Four well supported lineages within Leptonetidae (new status) are recovered: (1) the Calileptoneta group, (2) the Leptoneta group, (3) the Paraleptoneta group, and (4) the Protoleptoneta group. Most genera within Leptonetidae are monophyletic, although Barusia, Cataleptoneta, and Leptoneta include misplaced species and require taxonomic revision. The origin of Archoleptonetidae (new rank), Leptonetidae, and the four main lineages within Leptonetidae date to the Cretaceous. DEC analysis infers the Leptoneta and Paraleptoneta groups to have ancestral distributions restricted to Mediterranean Europe, whereas the Calileptoneta and Protoleptoneta groups include genera with ancestral distributions spanning eastern and western North America, Mediterranean Europe, and east Asia. Based on a combination of biology, estimated divergence times, and inferred ancestral distributions we hypothesise that Leptonetidae was once widespread across the Holarctic and their present distributions are largely the result of vicariance. Given the wide disjunctions between taxa, we broadly interpret the family as a Holarctic relict fauna and hypothesise that they were once part of the Boreotropical forest ecosystem.
... Therefore, the LTT plot and histogram of the higher-level diversification of bee flies provide sufficient evidence to demonstrate the increased diversification rate (Fig. 5A). A similar increased level of diversification during this hot geological period has been detected in spiders (Shao and Li, 2018), ants (Moreau et al., 2006), and more Fig. 6. Set of distinct diversification rate-shift configurations sampled by BAMM during simulation of the posterior probabilities. ...
Bombyliidae is a very species‐rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present‐day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the main lineages in our AHE tree to build a data set with more genes (550 loci versus 216 loci) and higher support levels. Our overall results show strong congruence with the current classification of the family, with 11 out of 14 included subfamilies recovered as monophyletic. Heterotropinae and Mythicomyiinae are successive sister groups to the remainder of the family. We examined the evolution of key morphological characters through our phylogenetic hypotheses and show that neither the “sand chamber subfamilies” nor the “Tomophthalmae” are monophyletic in our phylogenomic analyses. Based on our results, we reinstate two tribes at the subfamily level (Phthiriinae stat. rev. and Ecliminae stat. rev.) and we include the genus Sericosoma Macquart (previously incertae sedis) in the subfamily Oniromyiinae, bringing the total number of bee fly subfamilies to 19. Our dating analyses indicate a Jurassic origin of the family (165–194 Ma), with the sand chamber evolving early in bee fly evolution, in the late Jurassic or mid‐Cretaceous (100–165 Ma). We hypothesize that the angiosperm radiation and the hothouse climate established during the late Cretaceous accelerated the diversification of bee flies, by providing an expanded range of resources for the parasitoid larvae and nectarivorous adults.
... Magalhaes et al., 2020). Different studies have used it as either a stem linyphiid (Kuntner et al., 2013;Dimitrov et al., 2017;Fern andez et al., 2018;Shao and Li, 2018), a crown linyphiid (Scharff et al., 2020), a crown clade containing all linyphiids except Stemonyphantes (Dimitrov et al., 2012;Benavides et al., 2016) or, more recently, a stem araneoid (Magalhaes et al., 2020). Although the synapomorphies currently defining the family Linyphiidae cannot be observed in the fossil specimen, the overall somatic morphology, and setation and spination patterns are similar to that of some of the members of the extant species of Agyneta and closely related taxa. ...
We report on the colonization and diversification of linyphiid spiders in the Pacific oceanic archipelago of Juan Fernandez. About 50 spider species occur naturally in these islands, most of them endemic and about half of them are linyphiids. Linyphiidae includes no fewer than 15 species of Laminacauda and three of Neomaso (with several additional undescribed species in the latter genus), all of them single island endemics. There are three additional linyphiid endemic genera, two monotypic and one, Juanfernandezia, with two species. Unlike the rather uniform somatic morphology and small ground sheet webs of the continental Laminacauda and Neomaso species, the Juan Fernandez endemics exhibit morphological features and life history traits that are very rare or unknown in any other linyphiids. A multi‐locus phylogenetic analysis confirms at least five independent Juan Fernandez colonizations of Linyphiidae, two within the same genus, and three of which underwent subsequent local diversification. Different calibrations suggest alternative colonization timelines, some at odds with island ages, but all agree on similar diversification timings of the endemic lineages. Rare phenotypic traits (e.g. gigantism, massive chelicerae or elongated legs) evolved multiple times independently within the islands. Based on the remarkable levels of eco‐phenotypic differentiation in locally diversified species showing densely packed distributions, we propose that Laminacauda, and probably Neomaso, constitute a case of adaptive radiation.
... The taxonomic sampling included 13 species of the genus Dysdera, 10 of them from the Canary Islands (eight from the western and central islands and two from the eastern ones); two species of Parachtes, which together with Dysdera belong to the Dysderinae subfamily; and one representative of each of the other two Dysderidae subfamilies, namely Harpacteinae and Rhodinae (Appendix 1). Second, we downloaded HTS data from most genomic and transcriptomic records belonging to the spider clade Synspermiata, to which the Dysderidae family belongs (Michalik & Ramírez, 2014), and one of its sister lineages, the family Hypochilidae Marx, 1888 (Fernández et al., 2018;Garrison et al., 2016;Shao & Li, 2018), available at the NCBI database. The transcriptomic dataset consisted of 33 records, representing the family Hypochilidae and 13 out of the 17 Synspermiata families. ...
The advent of high-throughput sequencing technologies (HTS) has generated an unprecedented
amount of genomic and transcriptomic information. A vast amount of
these data is not even used in targeted projects but is made available in public repositories.
Previous studies have demonstrated that HTS data constitute a valuable
resource to recover mitogenomic information, which is most relevant for studies of
non-model and undersampled taxa. The spider family Dysderidae exemplifies well
this situation: It is a highly diverse group, exceptionally well-suited for evolutionary
and ecological research, but with a sparse mitogenomic record. In this study, we used
public and in-house HTS data to assemble and annotate at no cost 13 complete and
6 partial Dysderidae mitogenomes, as well as 34 partial mitogenomes belonging to
other taxa within the Synspermiata clade, to which Dysderidae belongs. The mitogenomic
information was further used to interrogate on a diverse array of evolutionary
questions posed by the family. Phylogenetic inference clarified the evolutionary
scenario of the colonization of the Canary Islands by the genus Dysdera, supporting
two independent colonizations from the continent. Synteny analyses indicated that
gene organization at the mitogenomic level is overall conserved within Dysderidae,
the only exceptions being two cave-dwelling species, each of them with a unique putative
transposition not described before in spiders. Finally, tRNA secondary structure
reconstruction confirmed that the extreme compaction of tRNA is conserved
across the family, suggesting that its origin could be traced back to approximately
100 million years ago (Mya). Altogether, this study demonstrates the potential of
publicly available HTS data to conduct low-cost evolutionary research at different
biological levels.
... Our UCE phylogenies are also largely congruent with previous phylogenomic analyses (Fernández et al. 2018). Important taxon additions include the hypochilid Ectatosticta, thus recovering a monophyletic Hypochilidae, and two telemids, suggesting that this family is sister to Scytodoidea + Pholcoidea (as in Shao and Li 2018). Our dense sample of leptonetids suggests that this family is diphyletic, with Archoleptonetinae separate from Leptonetinae. ...
The common ancestor of spiders likely used silk to line burrows or make simple webs, with specialized spinning organs and aerial webs originating with the evolution of the megadiverse "true spiders" (Araneomorphae). The base of the araneomorph tree also concentrates the greatest number of changes in respiratory structures, a character system whose evolution is still poorly understood, and that might be related to the evolution of silk glands. Emphasizing a dense sampling of multiple araneomorph lineages where tracheal systems likely originated, we gathered genomic-scale data and reconstructed a phylogeny of true spiders. This robust phylogenomic framework was used to conduct maximum likelihood and Bayesian character evolution analyses for respiratory systems, silk glands, and aerial webs, based on a combination of original and published data. Our results indicate that in true spiders, posterior book lungs were transformed into morphologically similar tracheal systems six times independently, after the evolution of novel silk gland systems and the origin of aerial webs. From these comparative data we put forth a novel hypothesis that early-diverging web building spiders were faced with new energetic demands for spinning, which prompted the evolution of similar tracheal systems via convergence; we also propose tests of predictions derived from this hypothesis.
... Our diversification studies reveal an increase in speciation rates bracketed between the Permian and the Early Cretaceous, in the origin of most sub-ordinal clades, with no evidence of higher speciation rates coinciding with the early rapid arachnid cladogenesis. A heightened diversification of spiders during the Cretaceous has previously been detected, suggested to result from the rise of angiosperms, stimulated by a warmer climate that led to the proliferation of spiders' main prey, insects (Shao and Li, 2018). Interestingly, we did not observe an early burst of diversification at the origin of chelicerates followed by a slowdown toward the present, a statistical bias usually found in large clades that survive to the present, the so-called "push of the past" (Nee et al., 1994). ...
Understanding the temporal context of terrestrialization in chelicerates depends on whether terrestrial groups, the traditional Arachnida, have a single origin and whether or not horseshoe crabs are primitively or secondarily marine. Molecular dating on a phylogenomic tree that recovers arachnid monophyly, constrained by 27 rigorously vetted fossil calibrations, estimates that Arachnida originated during the Cambrian or Ordovician. After the common ancestor colonized the land, the main lineages appear to have rapidly radiated in the Cambrian–Ordovician boundary interval, coinciding with high rates of molecular evolution. The highest rates of arachnid diversification are detected between the Permian and Early Cretaceous. A pattern of ancient divergence estimates for terrestrial arthropod groups in the Cambrian while the oldest fossils are Silurian (seen in both myriapods and arachnids) is mirrored in the molecular and fossil records of land plants. We suggest the discrepancy between molecular and fossil evidence for terrestrialization is likely driven by the extreme sparseness of terrestrial sediments in the rock record before the late Silurian.
... Transcriptomic studies are getting us ever closer to having a well-supported higher level phylogeny of the spider tree of life. In these studies, most nodes are well resolved and there is a general congruence across studies about the relationships of the major lineages of spiders (Bond et al., 2014;Fernández, Hormiga, & Giribet, 2014;Fernández et al., 2018;Garrison et al., 2016;Shao & Li, 2018). However, no other independent data set comparable to that of transcriptomes has been used for resolving the higher level relationships of spiders. ...
Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target‐capture methods, using the previously designed arachnid‐specific probe‐set, can target a maximum of about 1,000 loci. Here, we develop a specialized target‐capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. We designed the “spider‐specific” probe set using three spider genomes (Loxosceles, Parasteatoda and Stegodyphus) and ensured that the newly designed probe‐set include UCEs from the previously designed Arachnida probe set. The new “spider‐specific” probes were used to sequence UCE loci in 51 specimens. The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. The “spider‐specific” probes were also used to gather loci from a total of 84 representative taxa across Araneae. On mapping these 84 taxa to the Arachnida probe set, we captured at most 710 UCE loci, while the spider specific probe set captured up to 1,547 UCE loci from the same taxon sample. Phylogenetic analyses using Maximum Likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g., UCE data suggests monophyly of “symphytognathoids”). Our preferred analysis based on topology tests, suggests monophyly of the “symphytognathoids” (the miniature orb‐weavers), which in previous studies has only been supported by a combination of morphological and behavioral characters.
... Analyses of disparity and morphological variation may lack explanatory power if not conducted in a phylogenetic context. While overarching spider phylogeny is improving all the time (Garrison et al. 2016;Dimitrov et al. 2017;Wheeler et al. 2017;Fernández et al. 2018;Shao and Li 2018), uncertainty remains concerning the relationships of many genera. In Araneidae, recent works (Gregorič et al. 2015;Scharff et al. 2019) have repudiated some previous hypotheses (e.g., Scharff and Coddington 1997) and supported new clades based on nucleotide sequence data as well as morphology and behavior. ...
Sexual size dimorphism in orb-weaving spiders is a relatively well-studied phenomenon, and numerous works have documented evolutionary variation in interspecific size and degree of dimorphism. To date, these studies have been largely limited to assessing the evolution of a single or few linear measurements correlated with body size. While the descriptive and comparative literature is rich with qualitative and linear comparisons that distinguish the sexes and characterize species, the extent to which interspecific or dimorphic variation in size correlates with morphological shape remains relatively unexplored. The carapace of spiders is generally conserved in shape, especially among members of the same family, but is neither well-characterized as a potential facet of spider sexual dimorphism nor as a variable structure overall. Here, we use geometric morphometric techniques to quantify differences in carapace shape among members of the family Araneidae and test for allometric influences on interspecific and dimorphic shape differences across orb-weavers. We show that females and males differ in shape, occupying overlapping but distinct areas of morphospace, with males having more piriform carapaces than females. Araneid spider subfamilies overlap substantially in morphospace, though interspecific differences in shape are generally greater than those distinguishing males and females of a species. Furthermore, we show that female carapace shape shows phylogenetic signal and is more conserved than is male shape. Carapace shape differences made evident from canonical variates analysis are congruent with the more mobile lifestyle adopted by males, as a broader carapace may support more robust leg musculature.
... Psilodercids were elevated to family rank by Wunderlich (2004Wunderlich ( , 2008. Recently, phylogenetic analyses suggest that Psilodercidae are the sister group to the lineage encompassing Sicariidae Keyserling, 1880 and Scytodidae Blackwall, 1864 (Shao and Li 2018). ...
Four new species are described in two psilodercid genera, Qiongocera Li & Li, 2017 and Relictocera Li & Li, 2017: Qiongocera luoxuan Li & Li, sp. nov. (♂♀) from China, Relictocera wugen Li & Li, sp. nov. (♂♀) and R. sigen Li & Li, sp. nov. (♂) from Vietnam, and R. qianzi Li & Li, sp. nov. (♂♀) from Thailand. These genera were previously thought to be monotypic. In addition, one species of the genus Merizocera Fage, 1912 is transferred to Relictocera: Relictocera mus (Deeleman-Reinhold, 1995), comb. nov. (♂♀). The types of the new species are deposited in the Institute of Zoology, Chinese Academy of Sciences (IZCAS) in Beijing.
... Leptonetids are generally tiny spiders (1.0-3.0mm) that build an irregular and fairly large space-web and often carry their egg sacs or hang them beneath the webs (Lin & Li, 2010). Although traditionally considered haplogyne spiders, recent phylogenomic studies have revealed that leptonetids are more closely related to the entelegynes (Garrison et al, 2016;Fernández & Hormiga, 2018;Shao & Li, 2018). They can be distinguished from other spider families by a distinctive six-eyed pattern with the posterior median eyes separated from the strongly recurved anterior and posterior lateral eyes. ...
Three new species of the spider family Leptonetidae from caves in Hunan Province, China are described: Leptonetela biocellata sp. nov., Leptonetela latapicalis sp. nov. and Leptonetela tangi sp. nov. Detailed illustrations of the three new species are provided.
Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalisation to partition ancestral functions and/or neofunctionalisation to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterised the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organisation while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalisation between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the interrelationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoi-dea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
Spiders are among the most varied terrestrial predators, with highly diverse morphology, ecology, and behavior. Morphological and molecular data have greatly contributed to advances in the phylogeny and evolutionary dynamics of spiders. Here, we performed comprehensive mitochondrial phylogenomics analysis on 78 mitochondrial genomes (mitogenomes) representing 29 families; of these, 23 species from eight families were newly generated. Mesothelae retained the same gene arrangement as the arthropod ancestor ( Limulus polyphemus), while Opisthothelae showed extensive rearrangement, with 12 rearrangement types in transfer RNAs (tRNAs) and control region. Most spider tRNAs were extremely truncated and lacked typical dihydrouridine or TΨC arms, showing high tRNA structural diversity; in particular, trnS1 exhibited anticodon diversity across the phylogeny. The evolutionary rates of mitochondrial genes were potentially associated with gene rearrangement or truncated tRNAs. Both mitogenomic sequences and rearrangements possessed phylogenetic characteristics, providing a robust backbone for spider phylogeny, as previously reported. The monophyly of suborder, infraorder, retrolateral tibial apophysis clade, and families (except for Pisauridae) was separately supported, and high-level relationships were resolved as (Mesothelae, (Mygalomorphae, (Entelegynae, (Synspermiata, Hypochilidae)))). The phylogenetic positions of several families were also resolved (e.g., Eresidae, Oecobiidae and Titanoecidae). Two reconstructions of ancestral web type obtained almost identical results, indicating that the common ancestor of spiders likely foraged using a silk-lined burrow. This study, the largest mitochondrial phylogenomics analysis of spiders to date, highlights the usefulness of mitogenomic data not only for providing efficient phylogenetic signals for spider phylogeny, but also for characterizing trait diversification in spider evolution.
Whole genome duplications have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signalling pathway components and microRNAs are frequently retained as duplicates (so called ohnologs) following whole-genome duplication. These not only provide the best evidence for whole-genome duplication, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate whole-genome duplication, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt and frizzled, across these and twelve existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate whole-genome duplication. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with inter-order variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.
Beetles (Coleoptera) are the most diverse and species-rich group of insects, and a robust, time-calibrated phylogeny is fundamental to understanding macroevolutionary processes that underlie their diversity. Here we infer the phylogeny and divergence times of all major lineages of Coleoptera by analyzing 95 protein-coding genes in 373 beetle species, including ~67% of the currently recognized families. The subordinal relationships are strongly supported as Polyphaga (Adephaga (Archostemata, Myxophaga)). The series and superfamilies of Polyphaga are mostly monophyletic. The species-poor Nosodendridae is robustly recovered in a novel position sister to Staphyliniformia, Bostrichiformia, and Cucujiformia. Our divergence time analyses suggest that the crown group of extant beetles occurred ~297 million years ago (Mya) and that ~64% of families originated in the Cretaceous. Most of the herbivorous families experienced a significant increase in diversification rate during the Cretaceous, thus suggesting that the rise of angiosperms in the Cretaceous may have been an 'evolutionary impetus' driving the hyperdiversity of herbivorous beetles.
We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups. The dataset includes six markers from the mitochondrial (12S, 16S, COI) and nuclear (histone H3, 18S, 28S) genomes, and was analysed by multiple methods, including constrained analyses using a highly supported backbone tree from transcriptomic data. We recover most of the higher-level structure of the spider tree with good support, including Mesothelae, Opisthothelae, Mygalomorphae and Araneomorphae. Several of our analyses recover Hypochilidae and Filistatidae as sister groups, as suggested by previous transcriptomic analyses. The Synspermiata are robustly supported, and the families Trogloraptoridae and Caponiidae are found as sister to the Dysderoidea. Our results support the Lost Tracheae clade, including Pholcidae, Tetrablemmidae, Diguetidae, Plectreuridae and the family Pacullidae (restored status) separate from Tetrablemmidae. The Scytodoidea include Ochyroceratidae along with Sicariidae, Scytodidae, Drymusidae and Periegopidae; our results are inconclusive about the separation of these last two families. We did not recover monophyletic Austrochiloidea and Leptonetidae, but our data suggest that both groups are more closely related to the Cylindrical Gland Spigot clade rather than to Synspermiata. Palpimanoidea is not recovered by our analyses, but also not strongly contradicted. We find support for Entelegynae and Oecobioidea (Oecobiidae plus Hersiliidae), and ambiguous placement of cribellate orb-weavers, compatible with their non-monophyly. Nicodamoidea (Nicodamidae plus Megadictynidae) and Araneoidea composition and relationships are consistent with recent analyses. We did not obtain resolution for the titanoecoids (Titanoecidae and Phyxelididae), but the Retrolateral Tibial Apophysis clade is well supported. Penestomidae, and probably Homalonychidae, are part of Zodarioidea, although the latter family was set apart by recent transcriptomic analyses. Our data support a large group that we call the marronoid clade (including the families Amaurobiidae, Desidae, Dictynidae, Hahniidae, Stiphidiidae, Agelenidae and Toxopidae). The circumscription of most marronoid families is redefined here. Amaurobiidae include the Amaurobiinae and provisionally Macrobuninae. We transfer Malenellinae (Malenella, from Anyphaenidae), Chummidae (Chumma) (new syn.) and Tasmarubriinae (Tasmarubrius, Tasmabrochus and Teeatta, from Amphinectidae) to Macrobuninae. Cybaeidae are redefined to include Calymmaria, Cryphoeca, Ethobuella and Willisius (transferred from Hahniidae), and Blabomma and Yorima (transferred from Dictynidae). Cycloctenidae are redefined to include Orepukia (transferred from Agelenidae) and Pakeha and Paravoca (transferred from Amaurobiidae). Desidae are redefined to include five subfamilies: Amphinectinae, with Amphinecta, Mamoea, Maniho, Paramamoea and Rangitata (transferred from Amphinectidae); Ischaleinae, with Bakala and Manjala (transferred from Amaurobiidae) and Ischalea (transferred from Stiphidiidae); Metaltellinae, with Austmusia, Buyina, Calacadia, Cunnawarra, Jalkaraburra, Keera, Magua, Metaltella, Penaoola and Quemusia; Porteriinae (new rank), with Baiami, Cambridgea, Corasoides and Nanocambridgea (transferred from Stiphidiidae); and Desinae, with Desis, and provisionally Poaka (transferred from Amaurobiidae) and Barahna (transferred from Stiphidiidae). Argyroneta is transferred from Cybaeidae to Dictynidae. Cicurina is transferred from Dictynidae to Hahniidae. The genera Neoramia (from Agelenidae) and Aorangia, Marplesia and Neolana (from Amphinectidae) are transferred to Stiphidiidae. The family Toxopidae (restored status) includes two subfamilies: Myroinae, with Gasparia, Gohia, Hulua, Neomyro, Myro, Ommatauxesis and Otagoa (transferred from Desidae); and Toxopinae, with Midgee and Jamara, formerly Midgeeinae, new syn. (transferred from Amaurobiidae) and Hapona, Laestrygones, Lamina, Toxops and Toxopsoides (transferred from Desidae). We obtain a monophyletic Oval Calamistrum clade and Dionycha; Sparassidae, however, are not dionychans, but probably the sister group of those two clades. The composition of the Oval Calamistrum clade is confirmed (including Zoropsidae, Udubidae, Ctenidae, Oxyopidae, Senoculidae, Pisauridae, Trechaleidae, Lycosidae, Psechridae and Thomisidae), affirming previous findings on the uncertain relationships of the “ctenids” Ancylometes and Cupiennius, although a core group of Ctenidae are well supported. Our data were ambiguous as to the monophyly of Oxyopidae. In Dionycha, we found a first split of core Prodidomidae, excluding the Australian Molycriinae, which fall distantly from core prodidomids, among gnaphosoids. The rest of the dionychans form two main groups, Dionycha part A and part B. The former includes much of the Oblique Median Tapetum clade (Trochanteriidae, Gnaphosidae, Gallieniellidae, Phrurolithidae, Trachelidae, Gnaphosidae, Ammoxenidae, Lamponidae and the Molycriinae), and also Anyphaenidae and Clubionidae. Orthobula is transferred from Phrurolithidae to Trachelidae. Our data did not allow for complete resolution for the gnaphosoid families. Dionycha part B includes the families Salticidae, Eutichuridae, Miturgidae, Philodromidae, Viridasiidae, Selenopidae, Corinnidae and Xenoctenidae (new fam., including Xenoctenus, Paravulsor and Odo, transferred from Miturgidae, as well as Incasoctenus from Ctenidae). We confirm the inclusion of Zora (formerly Zoridae) within Miturgidae.
A new global temperature curve illustrates the change in global average temperature during the last 540 million years. This diagram updates and replaces the temperature curve of Scotese et al. (1999) based on Frakes (1992). The new curve combines geological data and oxygen isotope data. Lithologic indicators of climate such as evaporites, tillites, and coals can be used to map ancient climate zones (Tropical Everwet, Arid, Warm Temperate, Boreal Tropical, Cool Temperate, and Polar; Boucot et al., 2013). During the Phanerozoic the width of these climatic zones changed as the Earth’s climate moved from hothouse to icehouse conditions. Oxygen isotope measurements can accurately estimate the temperature of subtropical surface waters, which varied from 25˚C (77˚F) to 32˚C (90˚F) during icehouse/hothouse times. By combining global temperature estimates from geological data with estimates of tropical temperatures obtained from oxygen isotope studies, it is possible to produce an estimate of the global average temperature for any time in the past. In summary, the modern global average temperature is 14.5˚C (58˚F). The average global temperature for the last 540 million years is ~20˚C (68˚F), but the temperature has fluctuated between 25˚C (77˚F)(hothouse) and 10˚C (50˚F)(icehouse). During the Permo-Triassic Extinction, the global temperature spiked above 28˚C (82˚F). Most of the time, the global temperature gently rises and falls in response to gradual changes in orbital and solar parameters, ocean currents, sea level, atmospheric chemistry (greenhouse gases), and other factors. These changes occur over millions of years. Rarely, there is a drastic change in one of these factors resulting in either rapid global warming (Kidder–Worsley events) or rapid global cooling (Stoll-Schrag events). These abrupt climate excursions take place over thousands of years, rather than millions of years. We are currently living through the beginning of a Kidder-Worlsey event that may ultimately raise the global average temperature to ~20˚C (68˚F). In 5000-10,000 years, the global temperature will return to somewhat cooler (~18˚C , 64˚F) equilibrium state. An animation of changing climatic zones and global average temperature (0-540 million years) can be viewed at: https://www.youtube.com/watch?v=Oo1vbGCUR8s .
Molecular data along with fossils are being used increasingly to recover time-calibrated phylogenetic trees. Recently there have been manuscripts that have used divergence dating to understand evolutionary history of certain clades within Odonata (dragonflies and damselflies), yet the number of such articles is still low. We examined the Odonata fossil record and made a list of fossils that can be used for divergence time analysis. In this manuscript we provide a detailed review of the known crown group fossils for the order Odonata and nine nodes within this clade: Zygoptera, Epiprocta, Anisoptera, Aeshnidae, Gomphidae, Cavilabiata, Macromiidae, Corduliidae, and Libellulidae.
We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family Synaphridae. We use the resulting phylogenetic framework to study web evolution in araneoids. Araneoidea is monophyletic and sister to Nicodamoidea rank. n. Orbiculariae are not monophyletic and also include the RTA clade, Oecobiidae and Hersiliidae. Deinopoidea is paraphyletic with respect to a lineage that includes the RTA clade, Hersiliidae and Oecobiidae. The cribellate orb-weaving family Uloboridae is monophyletic and is sister group to a lineage that includes the RTA Clade, Hersiliidae and Oecobiidae. The monophyly of most Araneoidea families is well supported, with a few exceptions. Anapidae includes holarchaeids but the family remains diphyletic even if Holarchaea is considered an anapid. The orb-web is ancient, having evolved by the early Jurassic; a single origin of the orb with multiple “losses” is implied by our analyses. By the late Jurassic, the orb-web had already been transformed into different architectures, but the ancestors of the RTA clade probably built orb-webs. We also find further support for a single origin of the cribellum and multiple independent losses. The following taxonomic and nomenclatural changes are proposed: the cribellate and ecribellate nicodamids are grouped in the superfamily Nicodamoidea rank n. (Megadictynidae rank res. and Nicodamidae stat. n.). Araneoidea includes 17 families with the following changes: Araneidae is re-circumscribed to include nephilines, Nephilinae rank res., Arkyidae rank n., Physoglenidae rank n., Synotaxidae is limited to the genus Synotaxus, Pararchaeidae is a junior synonym of Malkaridae (syn. n.), Holarchaeidae of Anapidae (syn. n.) and Sinopimoidae of Linyphiidae (syn. n.).
The morphological, physiological, and behavioural traits of organisms are often used as surrogates for actual ecological functions. However, differences in these traits do not necessarily lead to functional differences and/or can be context–dependent. Therefore, it is necessary to explicitly test whether the surrogates have general ecological relevance. To investigate the relationship between the hunting strategies of predators (i.e. how, where, and when they hunt) and their function, we used euryphagous spiders as model group. We used published data on the diet composition of 76 spider species based on natural prey and laboratory prey acceptance experiments. We computed differences in the position and width of trophic niches among pairs of sympatrically occurring species. Pairs were made at different classification levels, ranked according to the dissimilarity in their hunting strategies: congeners, confamiliars (as phylogenetic proxies for similarity in hunting strategy), species form the same main class of hunting strategy, from the same supra-class, and from different supra-classes. As for niche position computed from the natural prey analyses, species from the same class differed less than species from different classes. A similar pattern was obtained from the laboratory studies, but the congeners differed less than the species from the same classes. Niche widths were most similar among congeners and dissimilar among species from different supra-classes. Functional differences among euryphagous spiders increased continuously with increasing difference in their hunting strategy. The relative frequency of hunting strategies within spider assemblages can, therefore, influence the food webs through hunting strategy-specific predator-prey interactions.
Motivation:
We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction.
Results:
The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment.
Availability and implementation:
The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/ CONTACT: katoh@ifrec.osaka-u.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.
Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves-a clade that encompasses nearly all living bird species-remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades-Columbea and Passerea-were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction.
The oldest fossil mygalomorph spider, from the Anisian Gres a Voltzia of the northern Vosges, is described Rosamygale grauvogeli gen. et sp. nov. The spider exhibits mainly plesiomorphic characters. It is a tuberculote (sensu Raven 1985) and is placed in the Hexathelidae, with some reservations. A ground-dwelling spider, Rosamygale was an integral part of the halophilous terrestrial biota of the time. The spiders became entombed in the wet sediment of desiccating pools. The presence of a primitive tuberculote on the southern margins of the Zechstein Sea in the Middle Triassic is evidence for a pan-Pangaean distribution of the Mygalomorphae prior to the break-up of the supercontinent. -Authors
Subject Category: Biology (whole organism) Subject Areas: palaeontology/taxonomy and systematics/evolution The rich fossil record of Crocodyliformes shows a much greater diversity in the past than today in terms of morphological disparity and occupation of niches. We conducted topology-based analyses seeking diversification shifts along the evolutionary history of the group. Our results support previous studies, indicating an initial radiation of the group following the Triassic/Jurassic mass extinction, here assumed to be related to the diversification of terrestrial protosuchians, marine thalattosuchians and semi-aquatic lineages within Neosuchia. During the Cretaceous, notosuchians embodied a second diversification event in terrestrial habitats and eusuchian lineages started diversifying before the end of the Mesozoic. Our results also support previous arguments for a minor impact of the Cretaceous/Palaeogene mass extinction on the evolutionary history of the group. This argument is not only based on the information from the fossil record, which shows basal groups surviving the mass extinction and the decline of other Mesozoic lineages before the event, but also by the diversification event encompassing only the alligatoroids in the earliest period after the extinction. Our results also indicate that, instead of a continuous process through time, Crocodyliformes diversification was patchy, with events restricted to specific subgroups in particular environments and time intervals.
This study describes a new spider with the most numerous specimens (c. two-thirds) known from the Middle Jurassic Jiulongshan Formation of Daohugou, China, as Zhizhu daohugouensis gen. et sp. nov, together with a related form from the Early Cretaceous Yixian Formation of Huangbanjigou, Zhizhu jeholensis sp. nov., and another, unnamed, specimen known only from an immature female from Daohugou. These spiders are all placed in the stem-Deinopoidea. Two recent studies of the phylogeny of spiders using phylogenomics have shown that deinopoids may be closer to non-orb-weaving cribellates than to ecribellate orbicularians, and that if the evolution of the orb web is a unique event, then it occurred deeper in time, perhaps among early Mesozoic cribellates such as these. The new spiders described here contribute to knowledge of the biodiversity and palaeoecology of the forested lake margins of the North China Block in mid-Mesozoic times.
Plants have a long evolutionary history, during which mass extinction events dramatically affected Earth's ecosystems and its biodiversity. The fossil record can shed light on the diversification dynamics of plant life and reveal how changes in the origination–extinction balance have contributed to shaping the current flora.
We use a novel Bayesian approach to estimate origination and extinction rates in plants throughout their history. We focus on the effect of the ‘Big Five’ mass extinctions and on estimating the timing of origin of vascular plants, seed plants and angiosperms.
Our analyses show that plant diversification is characterized by several shifts in origination and extinction rates, often matching the most important geological boundaries. The estimated origin of major plant clades predates the oldest macrofossils when considering the uncertainties associated with the fossil record and the preservation process.
Our findings show that the commonly recognized mass extinctions have affected each plant group differently and that phases of high extinction often coincided with major floral turnovers. For instance, after the Cretaceous–Paleogene boundary we infer negligible shifts in diversification of nonflowering seed plants, but find significantly decreased extinction in spore‐bearing plants and increased origination rates in angiosperms, contributing to their current ecological and evolutionary dominance.
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved.
We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences,
with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent
results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician
[~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian
(~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides
a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Significance
Angiosperm range expansion and diversification have been major biotic upheavals in the Earth history. Mechanisms involved in their successful diversification have mainly called upon intrinsic processes at the plant level, leaving the influence of the global tectonics poorly explored. We investigate evolution of paleogeography and climate and correlate it with the diversification of angiosperms by using a general circulation model. We show that Pangea breakup induced an important expansion of temperate zones during the late Cretaceous which was concomitant to the rise of angiosperms. We suggest that the breakup of Pangea led to the onset of new humid bioclimatic continents, which in turn may have provided new external conditions for ecological expansion of the angiosperms and their diversification.
Dating the Opiliones tree of life has become an important enterprise for this group of arthropods, due to their ancient origins and important biogeographic implications. To incorporate both methodological innovations in molecular dating as well as new systematic discoveries of harvestman diversity, we conducted total evidence dating on a data set uniting morphological and/or molecular sequence data for 47 Opiliones species, including all four well-known Palaeozoic fossils, to test the placement of both fossils and newly discovered lineages in a single analysis. Furthermore, we investigated node dating with a phylogenomic data set of 24,202 amino acid sites for 14 species of Opiliones, sampling all extant suborders. In this way, we approached molecular dating of basal harvestman phylogeny using different data sets and approaches to assess congruence of divergence time estimates. In spite of the markedly different composition of data sets, our results show congruence across all analyses for age estimates of basal nodes that are well constrained with respect to fossil calibrations (e.g., Opiliones, Palpatores). By contrast, derived nodes that lack fossil calibrations (e.g., the suborders Cyphophthalmi, and Laniatores) have large uncertainty intervals in diversification times, particularly in the total evidence dating analysis, reflecting the dearth of calibration points and undersampling of derived lineages. Total evidence dating consistently produced older median ages than node dating for ingroup nodes, due to the nested placement of multiple Palaeozoic fossils. Our analyses support basal diversification of Opiliones in the Ordovician-Devonian period, corroborating the inferred ancient origins of this arthropod order, and underscore the importance of diversity discovery—both paleontological and neontological—in evolutionary inference.
While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used 'phylogenetic signal dissection' to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.
The correlation between species diversification and morphological evolution has long been of interest in evolutionary biology. We investigated the relationship between these processes during the radiation of 250+ scincid lizards that constitute Australia's most species-rich clade of terrestrial vertebrates. We generated a time-calibrated phylogenetic tree for the group that was more than 85% complete at the species level and collected multivariate morphometric data for 183 species. We reconstructed the dynamics of species diversification and trait evolution using a Bayesian statistical framework (BAMM) that simultaneously accounts for variation in evolutionary rates through time and among lineages. We extended the BAMM model to accommodate time-dependent phenotypic evolution, and we describe several new methods for summarizing and visualizing macroevolutionary rate heterogeneity on phylogenetic trees. Two major clades (Lerista, Ctenotus; > 90 spp. each) are associated with high rates of species diversification relative to the background rate across Australian sphenomorphine skinks. The Lerista clade is characterized by relatively high lability of body form and has undergone repeated instances of limb reduction, but Ctenotus is characterized by an extreme deceleration in the rate of body shape evolution. We estimate that rates of phenotypic evolution decreased by more than an order of magnitude in the common ancestor of the Ctenotus clade. These results provide evidence for a modal shift in phenotypic evolutionary dynamics and demonstrate that major axes of morphological variation can be decoupled from species diversification. More generally, the Bayesian framework described here can be used to identify and characterize complex mixtures of dynamic processes on phylogenetic trees.
The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
The phylogeny of the spider family Sparassidae is comprehensively investigated for the first time using four molecular markers (mitochondrial COI and 16S; nuclear H3 and 28S). Sparassidae was recovered as monophyletic and as most basal group within the RTA-clade. The higher-level clade Dionycha was not but monophyly of RTA-clade was supported. No affiliation of Sparassidae to other members of the 'Laterigradae' (Philodromidae, Selenopidae and Thomisidae) was observed, and the crab-like posture of this group assumed a result of convergent evolution. Only Philodromidae and Selenopidae were found members of a supported clade, but together with Salticidae and Corinnidae, while Thomisidae was nested within the higher Lycosoidea. Within Sparassidae monophyly of the subfamilies Heteropodinae sensu stricto, Palystinae and Deleninae was recovered. Sparianthinae was supported as the most basal clade within Sparassidae. Sparassinae and the genus Olios were found each to be polyphyletic. Eusparassinae was not recovered monophyletic, with the two original genera Eusparassus and Pseudomicrommata in separate clades and only the latter clustered with most other assumed Eusparassinae, here termed the "African clade". Further focus was on the monophyletic genus Eusparassus and its proposed species groups, of which the dufouri-, walckenaeri- and doriae-group were confirmed as monophyletic with the two latter groups more closely related. According to molecular clock analyses, the divergence time of Sparassidae and Eusparassus was estimated with 186 and 70 million years ago respectively.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
A large female spider, Nephila jurassica, was described from Middle Jurassic strata of north-east China and placed in the modern genus Nephila (family Nephilidae) on the basis of many morphological similarities, but, as with many ancient fossils, the single specimen lacked synapomorphies of the family (Selden et al. 2011). In order to test the placement within the nephilid phylogenetic tree, Kuntner et al. (2013) calibrated the molecular phylogeny using N. jurassica in three different scenarios based on inferred mitochondrial substitution rates. They concluded that N. jurassica fitted better as a stem orbicularian than a nephilid. Now, a giant male spider has been discovered at the same locality that yielded N. jurassica. The two sexes are considered conspecific based on their similar morphological features, size, and provenance. The male cannot be accommodated in Nephilidae because of its pedipalp morphology, so the new genus Mongolarachne and family Mongolarachnidae are erected for the species. Comparison with possibly related families show that Mongolarachnidae is most likely on the orbicularian stem, close to other cribellate orbicularians (e.g., Deinopoidea), which suggests a greater diversity of cribellate orbicularians during the Middle Jurassic.
Electronic supplementary material
The online version of this article (doi:10.1007/s00114-013-1121-7) contains supplementary material, which is available to authorized users.
The macroevolutionary history of the megadiverse insect order Lepidoptera remains little-known, yet coevolutionary dynamics with their angiospermous host plants are thought to have influenced their diversification significantly. We estimate the divergence times of all higher-level lineages of Lepidoptera, including most extant families. We find that the diversification of major lineages in Lepidoptera are approximately equal in age to the crown group of angiosperms and that there appear to have been three significant increases in diversification rates among Lepidoptera over evolutionary time: 1) at the origin of the crown group of Ditrysia about 150 million years ago (mya), 2) at the origin of the stem group of Apoditrysia about 120 mya and finally 3) a spectacular increase at the origin of the stem group of the quadrifid noctuoids about 70 mya. In addition, there appears to be a significant increase in diversification rate in multiple lineages around 90 mya, which is concordant with the radiation of angiosperms. Almost all extant families appear to have begun diversifying soon after the Cretaceous/Paleogene event 65.51 mya.
New megafossil and microfossil data indicate four episodes in the diversification of Silurian-Early Carboniferous land plants of South China, a relatively continuous regional record. Plant diversity increased throughout, but the rising curve was punctuated by three major falls. There were peaks of origination in the Ludlow-Pragian, Givetian, late Famennian and Visean and peaks of extinction in the Pragian-Emsian, Givetian and early Tournaisian. Speciation and extinction rates were highest in the Lochkovian-Pragian and became progressively lower in subsequent stages. High correlation coefficients indicate that these events are associated with the availability of land habitat contingent on eustatic variations and increasing numbers of cosmopolitan genera. Meanwhile, proportions of endemic genera declined gradually. Due to less endemism and more migrations, both speciation and species extinction rates reduced. The changes of diversity and the timing of the three extinctions of land plants in South China are similar to those known already from Laurussia. However, the largest events in the Lochkovian-Pragian and subsequent smaller ones have not been seen in the global pattern of plant evolution. These land plant events do not correspond well temporally with those affecting land vertebrates or marine invertebrates. In South China, the diversity curve of land plants is generally opposite to that of marine faunas, showing a strong effect of eustatic variations. The increasing diversity of both land vertebrates and plants was punctuated above the Devonian-Carboniferous boundary, known as Romer's Gap, implying common underlying constraints on macroevolution of land animals and plants.
Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed, and have been shown to significantly improve on classical single-matrix models. Compared to their finite counterparts, infinite mixtures have a greater expressivity. However, they are computationally more challenging. This has resulted in practical compromises in the design of infinite mixture models. In particular, a fast but simplified version of a Dirichlet process model over equilibirum frequency profiles implemented in PhyloBayes (Lartillot et al, 2007) has often been used in recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have been practically out of reach.We introduce an Message Passing Interface (MPI) version of PhyloBayes, implementing the Dirichlet process mixture models as well as more classical empirical matrices and finite mixtures. The parallelization is made efficient thanks to the combination of two algorithmic strategies: a partial Gibbs sampling update of the tree topology, and the use of a truncated stick-breaking representation for the Dirichlet process prior. The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models.PhyloBayes MPI is freely available from our website www.phylobayes.org.
New fossil spiders from Triassic rocks of South Africa and Virginia are described. Though lacking synapomorphies of Araneomorphae, certain features suggest they belong in that infraorder, and possibly in the superfamily Araneoidea. Thus, they represent the oldest known fossil araneomorphs and extend the fossil record of the infraorder by approximately 40 Ma to 225 Ma.
To discover interordinal relationships of living and fossil placental mammals and the time of origin of placentals relative
to the Cretaceous-Paleogene (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil and living species.
Combining these data with molecular sequences, we obtained a phylogenetic tree that, when calibrated with fossils, shows that
crown clade Placentalia and placental orders originated after the K-Pg boundary. Many nodes discovered using molecular data
are upheld, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon
of Primates, a close link between Proboscidea (elephants) and Sirenia (sea cows), and the monophyly of echolocating Chiroptera
(bats). Our tree suggests that Placentalia first split into Xenarthra and Epitheria; extinct New World species are the oldest
members of Afrotheria.
The majority of environments are dominated by flowering plants today, but it is uncertain how this dominance originated. This increase in angiosperm diversity happened during the Cretaceous period (ca. 145-65 Ma) and led to replacement and often extinction of gymnosperms and ferns. We propose a scenario for the rise to dominance of the angiosperms from the Barremian (ca. 130 Ma) to the Campanian (ca. 84 Ma) based on the European megafossil plant record. These megafossil data demonstrate that angiosperms migrated into new environments in three phases: (i) Barremian (ca. 130-125 Ma) freshwater lake-related wetlands; (ii) Aptian-Albian (ca. 125-100 Ma) understory floodplains (excluding levees and back swamps); and (iii) Cenomanian-Campanian (ca. 100-84 Ma) natural levees, back swamps, and coastal swamps. This scenario allows for the measured evolution of angiosperms in time and space synthesizing changes in the physical environment with concomitant changes in the biological environment. This view of angiosperm radiation in three phases reconciles previous scenarios based on the North American record. The Cretaceous plant record that can be observed in Europe is exceptional in many ways. (i) Angiosperms are well preserved from the Barremian to the Maastrichtian (ca. 65 Ma). (ii) Deposits are well constrained and dated stratigraphically. (iii) They encompass a full range of environments. (iv) European paleobotany provides many detailed studies of Cretaceous floras for analysis. These factors make a robust dataset for the study of angiosperm evolution from the Barremian to the Campanian that can be traced through various ecosystems and related to other plant groups occupying the same niches.
A harvestman (Arachnida: Opiliones) is described from the Early Devonian (Pragian) Rhynie cherts, Aberdeenshire, Scotland. Eophalangium sheari gen. et sp. nov. is the oldest known harvestman. The material includes both males and a female preserving, respectively, a cuticle-lined penis and ovipositor within the opisthosoma. Both these structures are of essentially modern appearance. The Rhynie fossils also show tracheae which are, again, very similar to those of living harvestmen. This is the oldest unequivocal record of arachnid tracheal respiration and indicates that E. sheari was terrestrial. An annulate, setose ovipositor in the female suggests that it can be excluded from the clades Dyspnoi and Laniatores, in which the ovipositor lacks such annulations. However, the penis shows evidence of two muscles, a feature of uncertain polarity seen in modern Troguloidea (Dyspnoi). The presence of median eyes and long legs excludes Cyphophthalmi, and thus, E. sheari is tentatively referred to the suborder Eupnoi. Therefore, this remarkable material is implicitly a crown-group harvestman and is one of the oldest known crown-group chelicerates. It also suggests an extraordinary degree of morphological stasis within the eupnoid line, with the Devonian forms differing little in gross morphology – and perhaps in reproductive behaviour – from their modern counterp
A new fossil Linyphiidae: Linyphiinae is described from 125-135 Ma old (Upper Neocomian-basal Lower Aptian) Cretaceous amber from the Kdeirji/Hammana outcrop, Lebanon. This is the oldest known linyphiid as well as the oldest described amber spider. The first major radiation of the linyphiid subfamilies occurred in the early Cretaceous, if not before, and the presence of Linyphiidae in this period predicts the presence of Pimoidae then too. Current evidence, which suggests the higher araneoids did not radiate and diversify until after the end-Cretaceous mass extinction event may be an artefact of sample size.
Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic. We find no significant association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade-the most diverse araneomorph spider lineage-shows enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle.
We combine statistical and phylogenetic approaches to test the hypothesis that adaptive radiation and key innovation have contributed to the diversity of the order Araneae. The number of unbalanced araneid clades (those whose species numbers differ by 90% or more) exceeds the number predicted by a null Markovian model. The current phylogeny of spider families contains 74 bifurcating nodes, of which 31 are unbalanced. As this is significantly more than the 14.8 expected unbalanced nodes, some of the diversity within the Araneae can be attributed to some deterministic cause (e.g., adaptive radiation). One of the more highly unbalanced (97%) bifurcations divides the orb-weaving spiders into the Deinopoidea and the larger Araneoidea. A simple statistical model shows that the inequality in diversity between the Deinopoidea and the Araneoidea is significant, and that it is associated with the replacement of primitive cribellar capture thread by viscous adhesive thread and a change from a horizontal to a vertical orb-web orientation. These changes improve an orb-web's ability to intercept and retain prey and expand the adaptive zone that orb-weaving spiders can occupy and are, therefore, considered to be "key innovations."
Introduction.- First Steps in R for Phylogeneticists.- Phylogenetic Data in R.- Plotting Phylogenies.- Phylogeny Estimation.- Analysis of Macroevolution with Phylogenies.- Developing and Implementing Phylogenetic Methods in R.
Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living bird species—remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10⁷ bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades—Columbea and Passerea—were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.
Ancestral state reconstruction (ASR) is a popular method for exploring the evolutionary history of traits that leave little or no trace in the fossil record. For example, it has been used to test hypotheses about the number of evolutionary origins of key life-history traits such as oviparity, or key morphological structures such as wings. Many studies that use ASR have suggested that the number of evolutionary origins of such traits is higher than was previously thought. The scope of such inferences is increasing rapidly, facilitated by the construction of very large phylogenies and life-history databases. In this paper, we use simulations to show that the number of evolutionary origins of a trait tends to be overestimated when the phylogeny is not perfect. In some cases, the estimated number of transitions can be several fold higher than the true value. Furthermore, we show that the bias is not always corrected by standard approaches to account for phylogenetic uncertainty, such as repeating the analysis on a large collection of possible trees. These findings have important implications for studies that seek to estimate the number of origins of a trait, particularly those that use large phylogenies that are associated with considerable uncertainty. We discuss the implications of this bias, and methods to ameliorate it. J. Exp. Zool. (Mol. Dev. Evol.) 9999B: 1-8, 2015. © 2015 Wiley Periodicals, Inc.
© 2015 Wiley Periodicals, Inc.
A set of experiments based on simulation and analysis found that using the parsimony algorithm for ancestral state estimation can benefit from increased sampling of terminal taxa. Estimation at the base of small clades showed strong sensitivity to tree topology and number of descendent tips. These effects were largely driven by the creation and negation of ambiguity across a topology. Root state and internal state estimation showed similar behavior. We conclude that increased taxon sampling density is generally advisable, and attention to topological effects may be advisable in evaluating the confidence placed in state estimation. We also explore the factors affecting ancestral state estimation and conjecture that as taxa are added to a tree, the total amount of information for root state estimation depends on the tree topology and distance to root state of added taxa. For a pure-birth model tree, we conjecture that the addition of N taxa increases root state information in proportion to log(N).
Phylogenetic relationships among archaeid spider lineages, as well as the placement of archaeids within the Araneomorphae, present a problem in the systematics of spiders. We investigate these relationships by broadly sampling taxa from the Araneomorphae and superfamily Palpimanoidea, as well as from extant and fossil archaeid lineages. Using parsimony and Bayesian methods we perform a total-evidence analysis that includes 126 morphological characters and over 4000 bases from one mitochondrial and three nuclear molecular markers. Phylogenetic analysis results in a delimitation of the superfamily Palpimanoidea to contain five families: Archaeidae, Mecysmaucheniidae, Stenochilidae, Palpimanidae and Huttoniidae. We also find the extant archaeids, which are restricted to the southern hemisphere, to be monophyletic, with the fossil archaeids paraphyletic. This phylogenetic framework is then used to interpret a novel morphological character, the highly modified and elevated cephalic area and elongated chelicerae (jaws), coupled with prey choice observations in the field and observations of chelicerae movements during predatory attacks. We conclude that the evolution of the elevated cephalic area, which reoriented the chelicerae muscles, led to highly manoeuvrable chelicerae and associated novel prey capture strategies. All members of Palpimanoidea appear to have modifications to the cephalic area, such as a diastema or sclerotization around the chelicerae bases, and furthermore, members appear to have evolved prey specialization.
Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported [1]. Current working hypotheses for a spider “backbone” phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype—the spider web.
Spiders constitute one of the most successful clades of terrestrial predators [1]. Their extraordinary diversity, paralleled only by some insects and mites [2], is often attributed to the use of silk, and, in one of the largest lineages, to stereotyped behaviors for building foraging webs of remarkable biomechanical properties [1]. However, our understanding of higher-level spider relationships is poor and is largely based on morphology [2, 3 and 4]. Prior molecular efforts have focused on a handful of genes [5 and 6] but have provided little resolution to key questions such as the origin of the orb weavers [1]. We apply a next-generation sequencing approach to resolve spider phylogeny, examining the relationships among its major lineages. We further explore possible pitfalls in phylogenomic reconstruction, including missing data, unequal rates of evolution, and others. Analyses of multiple data sets all agree on the basic structure of the spider tree and all reject the long-accepted monophyly of Orbiculariae, by placing the cribellate orb weavers (Deinopoidea) with other groups and not with the ecribellate orb weavers (Araneoidea). These results imply independent origins for the two types of orb webs (cribellate and ecribellate) or a much more ancestral origin of the orb web with subsequent loss in the so-called RTA clade. Either alternative demands a major reevaluation of our current understanding of the spider evolutionary chronicle.
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.
2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.
3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.
4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.
BaCoCa (BAse COmposition CAlculator) is a user-friendly software that combines multiple statistical approaches (like RCFV and C value calculations) to identify biases in aligned sequence data which potentially mislead phylogenetic reconstructions. As a result of its speed and flexibility, the program provides the possibility to analyze hundreds of pre-defined gene partitions and taxon subsets in one single process run. BaCoCa is command-line driven and can be easily integrated into automatic process pipelines of phylogenomic studies. Moreover, given the tab-delimited output style the results can be easily used for further analyses in programs like Excel or statistical packages like R. A built-in option of BaCoCa is the generation of heat maps with hierarchical clustering of certain results using R. As input files BaCoCa can handle FASTA and relaxed PHYLIP, which are commonly used in phylogenomic pipelines. BaCoCa is implemented in Perl and works on Windows PCs, Macs and Linux operating systems. The executable source code as well as example test files and a detailed documentation of BaCoCa are freely available at http://software.zfmk.de.
Ecologists have long searched for a framework of a priori species traits to help predict predator–prey interactions in food webs. Empirical evidence has shown that predator hunting mode and predator and prey habitat domain are useful traits for explaining predator–prey interactions. Yet, individual experiments have yet to replicate predator hunting mode, calling into question whether predator impacts can be attributed to hunting mode or merely species identity.
We tested the effects of spider predators with sit‐and‐wait, sit‐and‐pursue and active hunting modes on grasshopper habitat domain, activity and mortality in a grassland system. We replicated hunting mode by testing two spider predator species of each hunting mode on the same grasshopper prey species. We observed grasshoppers with and without each spider species in behavioural cages and measured their mortality rates, movements and habitat domains. We likewise measured the movements and habitat domains of spiders to characterize hunting modes.
We found that predator hunting mode explained grasshopper mortality and spider and grasshopper movement activity and habitat domain size. Sit‐and‐wait spider predators covered small distances over a narrow domain space and killed fewer grasshoppers than sit‐and‐pursue and active predators, which ranged farther distances across broader domains and killed more grasshoppers, respectively. Prey adjusted their activity levels and horizontal habitat domains in response to predator presence and hunting mode: sedentary sit‐and‐wait predators with narrow domains caused grasshoppers to reduce activity in the same‐sized domain space; more mobile sit‐and‐pursue predators with broader domains caused prey to reduce their activity within a contracted horizontal (but not vertical) domain space; and highly mobile active spiders led grasshoppers to increase their activity across the same domain area. All predators impacted prey activity, and sit‐and‐pursue predators generated strong effects on domain size.
This study demonstrates the validity of utilizing hunting mode and habitat domain for predicting predator–prey interactions. Results also highlight the importance of accounting for flexibility in prey movement ranges as an anti‐predator response rather than treating the domain as a static attribute.
Nee et al. (1994) presented likelihood equations for estimating speciation and extinction rates based on phylogenies of only extant species; in particular their method can infer extinction patterns without extinct species data. Meanwhile, even for the simplest model of speciation and extinction, namely the constant rate birth-death process, a number of studies have been published using different likelihood equations (Thompson, 1975; Rannala and Yang, 1996; Yang and Rannala, 1997; Gernhard, 2008; Stadler, 2009). The likelihood functions differ due to conditioning the likelihood on different quantities, like the age of the tree, survival of the tree, or the number of species in the tree.