Combining genomic, phenotypic and Sanger sequencing data to elucidate the phylogeny of the two-clawed spiders (Dionycha)

Infrequent Long-Range Dispersal and Evolution of a Top Terrestrial Arthropod Predator in the Sub-Antarctic

AbstractThe sub-Antarctic terrestrial ecosystems survive on isolated oceanic islands in the path of circumpolar currents and winds that have raged for more than 30 million years and are shaped by climatic cycles that surpass the tolerance limits of many species. Surprisingly little is known about how these ecosystems assembled their native terrestrial fauna and how such processes have changed over time. Here, we demonstrate the patterns and timing of colonization and speciation in the largest and dominant arthropod predators in the eastern sub-Antarctic: spiders of the genus Myro. Our results indicate that this lineage originated from Australia before the Plio-Pleistocenic glacial cycles and underwent an adaptive radiation on the Crozet archipelago, from where one native species colonized multiple remote archipelagos via the Antarctic circumpolar current across thousands of kilometers. The results indicate limited natural connectivity between terrestrial macroinvertebrate faunas in the eastern sub-Antarctic and partial survival of repeated glaciations in the Plio-Pleistocene. Furthermore, our findings highlight that by integrating arthropod taxa from multiple continents, the climatically more stable volcanic Crozet archipelago played a critical role in the evolution and distribution of arthropod life in the sub-Antarctic.

Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing

Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.

Burma Terrane Amber Fauna Shows Connections to Gondwana and Transported Gondwanan Lineages to the Northern Hemisphere (Araneae: Palpimanoidea)

Burmese amber is a significant source of fossils that documents the mid-Cretaceous biota. This deposit was formed around 99 Ma on the Burma Terrane, which broke away from Gondwana and later collided with Asia, although the timing is disputed. Palpimanoidea is a dispersal-limited group that was a dominant element of the Mesozoic spider fauna, and has an extensive fossil record, particularly from Burmese amber. Using morphological and molecular data, evolutionary relationships of living and fossil Palpimanoidea are examined. Divergence dating with fossils as terminal tips shows timing of diversification is contemporaneous with continental breakup.Ancestral range estimations show widespread ancestral ranges that divide into lineages that inherit different Pangean fragments, consistent with vicariance. Our results suggest that the Burmese amber fauna has ties to Gondwana due to a historical connection in the Early Cretaceous, and that the Burma Terrane facilitated biotic exchange by transporting lineages from Gondwana into the Holarctic in the Cretaceous.

Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies

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 inter-relationships 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, Palpimanoidea 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.

Taxonomic notes, distribution update and the first chromosomal analysis of Vectius niger (Simon, 1880) and Trochanteria gomezi Canals, 1933 (Araneae: Trochanteriidae)

Spiders of the family Trochanteriidae are characterized by the carapace being extremely flat, with a reflex border, medium posterior eyes flattened, laterigrade legs, the absence of claw tufts, anterior lateral spinnerets with an incomplete distal article, and an inflatable and epiginal plate formed by a divided plate. Two out of the six worldwide genera of Trocantheriids have species in the Brazilian areas: Trochanteria Karsch and Vectius Simon. Here we present the redescription of Vectius niger and morphological data of Trochanteria gomezi, with an expansion of the distribution of these species in the Neotropical region and unpublished chromosomal data of both species. Mitotic and meiotic cells of both T. gomezi and V. niger showed 2n=22 and 2n=24 telocentric chromosomes, with a sex chromosome system of the type X1X2 in males/X1X1X2X2 in females. The chromosomal data shown here matches those found in trochanteriids to date.

Revisions of Australian ground-hunting spiders VI: five new stripe-less miturgid genera and 48 new species (Miturgidae: Miturginae)

A group of Australian miturgines that are common in widespread areas of mostly dry landscapes are revised. Five new genera (Miturgopelma, Knotodo, Xistera, Miturgiella and Xeromiturga) and 48 new species are described. Three species presently included in three families are placed in these groups in the Miturgidae: Uliodon ferrugineus (L. Koch, 1873) is transferred from the Zoropsidae to Miturgopelma gen. nov.; likewise, Odo australiensis Hickman, 1944, from Central Australia, is transferred from an otherwise South American genus presently in the family Xenoctenidae to Miturgopelma gen. nov.; and Argoctenus gracilis Hickman, 1950 is transferred to Knotodo gen. nov. Miturgopelma gen. nov. is a very diverse genus found throughout much of drier Australia but not yet in Cape York, Queensland, although one species is taken from Tasmania. Besides Miturgopelma ferruginea (L. Koch, 1873) comb. nov. and Miturgopelma australiensis (Hickman, 1944) comb. nov., the new genus Miturgopelma includes 31 new species: M. alanyeni sp. nov., M. archeri sp. nov. M. baehrae sp. nov., M. bandalup sp. nov., M. biancahilleryae sp. nov., M. bogantungan sp. nov., M. brachychiton sp. nov., M. brevirostra sp. nov., M. bungabiddy sp. nov., M. buckaringa sp. nov., M. calperum sp. nov., M. caitlinae sp. nov., M. couperi sp. nov., M. culgoa sp. nov., M. echidna sp. nov., M. echinoides sp. nov., M. harveyi sp. nov., M. hebronae sp. nov., M. kinchega sp. nov., M. maningrida sp. nov., M. minderoo sp. nov., M. oakleigh sp. nov., M. paruwi sp. nov., M. rangerstaceyae sp. nov., M. rar sp. nov., M. rixi sp. nov., M. seida sp. nov., M. spinisternis sp. nov., M. watarrka sp. nov., M. woz sp. nov., and M. yarmina sp. nov. Knotodo gen. nov., a predominantly western and southern group, includes Knotodo gracilis (Hickman, 1950) comb. nov., and seven new species: K. coolgardie sp. nov., K. eneabba sp. nov., K. narelleae sp. nov., K. shoadi sp. nov., K. muckera sp. nov., K. nullarbor sp. nov., and K. toolinna sp. nov. Xistera gen. nov., another predominantly Western Australian and southern group, includes five new species: Xis. auriphila sp. nov., Xis. barlee sp. nov., Xis. coventryi sp. nov., Xis. jandateae sp. nov., and Xis. serpentine sp. nov. Xeromiturga gen. nov., another predominantly western and southern group, includes four new species: Xer. gumbardo sp. nov., Xer. mardathuna sp. nov., Xer. bidgemia sp. nov., and Xer. pilbara sp. nov. A widespread, monotypic eastern Australian genus, Miturgiella vulgaris gen. et sp. nov., is also described. Zoroides Berland, 1924, presently in Miturgidae, is considered a junior synonym of the phrurolithid Dorymetaecus Rainbow, 1920 syn. nov., thus making Dorymetaecus dalmasi (Berland 1924) comb. nov. Miturga whistleri Simon, 1909 and Miturga splendens Hickman, 1930 are both placed in Mituliodon tarantulinus syn. nov..

An Opiliones-specific ultraconserved element probe set with a near-complete family-level phylogeny

Sequence capture of ultraconserved elements (UCEs) has transformed molecular systematics across many taxa, with arachnids being no exception. The probe set available for Arachnida has been repeatedly used across multiple arachnid lineages and taxonomic levels, however more specific probe sets for spiders have demonstrated that more UCEs can be recovered with higher probe specificity. In this study, we develop an Opiliones-specific UCE probe set targeting 1915 UCEs using a combination of probes designed from genomes and transcriptomes, as well as the most useful probes from the Arachnida probe set. We demonstrate the effectiveness of this probe set across Opiliones with the most complete family-level phylogeny made to date, including representatives from 61 of 63 currently described families. We also test UCE recovery from historical specimens with degraded DNA, examine population-level data sets, and assess "backwards compatibility" with samples hybridized with the Arachnida probe set. The resulting phylogenies - which include specimens hybridized using both the Opiliones and Arachnida probe sets, historical specimens, and transcriptomes - are largely congruent with previous multi-locus and phylogenomic analyses. The probe set is also "backwards compatible", increasing the number of loci obtained in samples previously hybridized with the Arachnida probe set, and shows high utility down to shallow population-level divergences. This probe set has the potential to further transform Opiliones molecular systematics, resolving many long-standing taxonomic issues plaguing this lineage.

Taxonomic revision of the soldier spider genus Falconina Brignoli, 1985 (Araneae: Corinnidae: Corinninae)

The genus Falconina Brignoli, 1985 is revised and redescribed, including ten species. New records and documentation of morphological variation in F. gracilis (Keyserling, 1891) are presented; it and the type species, F. melloi (Schenkel, 1953), are rediagnosed. Falconina albomaculosa (Schmidt, 1971) is redescribed based on the female holotype and additional material from Ecuador, with the male being described for the first time. Falconina crassipalpis (Chickering, 1937) is redescribed based on the types and additional material from Barro Colorado, Panama. Six new species are described, diagnosed, and illustrated: F. iza sp. nov. ( from Rio Grande do Sul, Brazil); F. taita sp. nov. ( from Chapare and from Sapecho, Bolivia); F. catirina sp. nov. ( from Piau, Brazil); F. adriki sp. nov. ( and from Rio de Janeiro, Brazil); F. andresi sp. nov. ( from Meta, Colombia); and F. brignolii sp. nov. ( from Sucre, Venezuela). Additionally, distribution maps and an identification key to all of the known species of Falconina are provided.

Comparative Mitogenomics of Jumping Spiders with First Complete Mitochondrial Genomes of Euophryini (Araneae: Salticidae)

Salticidae is the most species-rich family of spiders with diverse morphology, ecology and behavior. However, the characteristics of the mitogenomes within this group are poorly understood with relatively few well-characterized complete mitochondrial genomes. In this study, we provide completely annotated mitogenomes for Corythalia opima and Parabathippus shelfordi, which represent the first complete mitogenomes of the tribe Euophryini of Salticidae. The features and characteristics of the mitochondrial genomes are elucidated for Salticidae by thoroughly comparing the known well-characterized mitogenomes. The gene rearrangement between trnL2 and trnN was found in two jumping spider species, Corythalia opima and Heliophanus lineiventris Simon, 1868. Additionally, the rearrangement of nad1 to between trnE and trnF found in Asemonea sichuanensis Song & Chai, 1992 is the first protein-coding gene rearrangement in Salticidae, which may have an important phylogenetic implication for the family. Tandem repeats of various copy numbers and lengths were discovered in three jumping spider species. The codon usage analyses showed that the evolution of codon usage bias in salticid mitogenomes was affected by both selection and mutational pressure, but selection may have played a more important role. The phylogenetic analyses provided insight into the taxonomy of Colopsus longipalpis (Żabka, 1985). The data presented in this study will improve our understanding of the evolution of mitochondrial genomes within Salticidae.

A novel probe set for the phylogenomics and evolution of RTA spiders

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.

Following the aridity: Historical biogeography and diversification of the Philodromidae spider genus Petrichus in South America

Aridity conditions and expansion of arid biomes in South America are closely linked to the onset of Andean orogeny since at least 30 Mya. Among arid-associated taxa, spiders belonging to the genus Petrichus are found along the Andes mountains and across the diagonal of open formations of the Chaco and Cerrado domains. In this contribution, we asked whether Petrichus originated prior to the central Andean uplift and what historical processes have promoted their diversification. We time-calibrated the phylogenetic tree of Philodromidae and estimated the divergence times of Petrichus. Considering phylogenetic uncertainty, we assessed biogeographical hypotheses of the historical events associated with the diversification of these spiders in South America. Petrichus originated along the Pacific coastal deserts in the Central Andes during the Early Miocene. The species likely dispersed from the western to the eastern side of the Andes coincidently with the central Andean uplift. The diversification of these spiders is coeval with the expansion of open grassland formations during the Late Miocene and Early Pliocene. Multiple dispersal events occurred from the Monte desert to southern South America and eastward to Chaco between ∼ 8 and 2.5 Mya. The Andes might have played a role as a corridor favoring geographical range expansions and colonization of new environments. In addition, we also suggest that Philodromidae might have an Oligocene origin or earlier. Future analyses based on further evidence and larger taxon sampling should be carried out to corroborate our findings.

Molecular phylogeny of the tropical wandering spiders (Araneae, Ctenidae) and the evolution of eye conformation in the RTA clade

Tropical wandering spiders (Ctenidae) are a diverse group of cursorial predators with its greatest species richness in the tropics. Traditionally, Ctenidae are diagnosed based on the presence of eight eyes arranged in three rows (a 2-4-2 pattern). We present a molecular phylogeny of Ctenidae, including for the first time representatives of all of its subfamilies. The molecular phylogeny was inferred using five nuclear (histone H3, 28S, 18S, Actin and ITS-2) and four mitochondrial (NADH, COI, 12S and 16S) markers. The final matrix includes 259 terminals, 103 of which belong to Ctenidae and represent 28 of the current 49 described genera. We estimated divergence times by including fossils as calibration points and biogeographic events, and used the phylogenetic hypothesis obtained to reconstruct the evolution of the eye conformation in the retrolateral tibial apophysis (RTA) clade. Ctenidae and its main lineages originated during the Paleocene-Eocene and have diversified in the tropics since then. However, in some analyses Ctenidae was recovered as polyphyletic as the genus Ancylometes Bertkau, 1880 was placed as sister to Oxyopidae. Except for Acantheinae, in which the type genus Acantheis Thorell, 1891 is placed inside Cteninae, the four recognized subfamilies of Ctenidae are monophyletic in most analyses. The ancestral reconstruction of the ocular conformation in the retrolateral tibial apophysis clade suggests that the ocular pattern of Ctenidae has evolved convergently seven times and that it has originated from ocular conformations of two rows of four eyes (4-4) and the ocular pattern of lycosids (4-2-2). We also synonymize the monotypic genus Parabatinga Polotov & Brescovit, 2009 with Centroctenus Mello-Leitão, 1929. We discuss some of the putative morphological synapomorphies of the main ctenid lineages within the phylogenetic framework offered by the molecular phylogenetic results of the study.