Research Article

Low coverage whole genome sequencing reveals a new subfamily of daddy long-legs spiders from Brazilian Caatinga (Araneae: Pholcidae)

Guanliang Meng^‡§, Leonardo S. Carvalho^|, Lars Podsiadlowski^‡, Bernhard A. Huber^‡

‡ Zoological Research Museum Alexander Koenig, Bonn, Germany

§ Institute of Zoology, Chinese Academy of Sciences, Beijing, China

| Universidade Federal do Piauí, Floriano, Brazil

Corresponding author: Bernhard A. Huber ( b.huber@leibniz-lib.de )

Academic editor: Lorenzo Prendini

This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Citation: Meng G, Carvalho LS, Podsiadlowski L, Huber BA (2026) Low coverage whole genome sequencing reveals a new subfamily of daddy long-legs spiders from Brazilian Caatinga (Araneae: Pholcidae). Arthropod Systematics & Phylogeny 84: 95-121. https://doi.org/10.3897/asp.84.e174748

ZooBank: urn:lsid:zoobank.org:pub:3F239F99-45DD-4B5A-9684-9B05109A6963

Abstract

Pholcid spiders have long been classified into five subfamilies, and this framework ultimately dates back to Eugène Simon’s non-phylogenetic system of 1893. While subfamily relationships and compositions have been updated extensively over the last decades, no new subfamily had to be erected for any of the hundreds of new species newly described since Simon. Here we report two new species from semi-arid Brazilian Caatinga: Caipira mineira Huber sp. nov., and Caipira baiana Huber sp. nov. Genomic data strongly support their sister-group relationship; we thus join them conservatively in a single genus, Caipira Huber gen. nov., even though they show some remarkable morphological differences. This genus is sister to a large clade including all pholcid subfamilies except Pholcinae and Smeringopinae, which necessitates the erection of a new subfamily: Caipirinae subfam. nov. In addition, we formalize the separation of the genus Artema from ‘other Arteminae’. This had previously been suggested by multi-locus genetic data, and is strongly supported by new genomic data. Arteminae is newly circumscribed to include only Artema and Priscula, and the name Physocyclinae subfam. nov. is proposed for ‘other Arteminae’. Pholcidae is thus divided into seven subfamilies, with the following relationships suggested by genomic data: (Pholcinae, Smeringopinae), (Caipirinae, ((Arteminae, Ninetinae), (Physocyclinae, Modisiminae))). Finally, we tested the hypothesis that the Chilean genus Aucana is the closest relative of the new Brazilian species. This is strongly rejected; Aucana is resolved as the only known South American representative of Physocyclinae.

Key words

Arteminae, Aucana, cave, morphology, phylogeny, Physocyclinae, relict, taxonomy

1. Introduction

Pholcidae are ubiquitous spiders in tropical and subtropical regions around the world. They occupy a wide range of different microhabitats, with corresponding variation in body size, body shape, leg length, and coloration (Eberle et al. 2018). More than 1,100 new species have been added to the family within the last 20 years, and assignments of new species to higher taxonomic ranks (subfamilies and genera) have usually been unproblematic. This is particularly true at the level of subfamilies, even though subfamily-level relationships and exact compositions of subfamilies have proven difficult to resolve in some cases. For example, relationships of Ninetinae to other subfamilies and the positions of the genera Artema Walckenaer, 1837 and Priscula Simon, 1893 at subfamily level have long been dubious (Huber 2000; Dimitrov et al. 2013; Eberle et al. 2018; Huber et al. 2018) and could only be resolved recently with genomic data (Meng et al. 2025).

Thus, the current subfamily division of Pholcidae is essentially an updated version of Simon’s (1893) classification, with numerous corrections and changes but without any new subfamily-level names (Huber 2011b). For more than a century, no new species have been discovered that would defy assignment to one of the subfamily-level taxa of Simon (1893) or their current emended versions. Here, we report on two newly discovered species for which genomic data suggest they are neither included into nor sister of an existing subfamily; thus, they require the creation of a new subfamily.

In addition, we formalize here the separation of Artema from ‘other Arteminae’, which was first suggested in Eberle et al. (2018) and which is strongly supported by new genomic data (Meng et al. 2025). We thus redefine Arteminae to include only Artema and Priscula and propose a new subfamily name for the ‘other Arteminae’ sensu Eberle et al. (2018) and Huber et al. (2018). Finally, we provide first molecular data for the Chilean genus Aucana Huber, because we initially thought (based on superficial similarity) that this genus might be the closest relative of the new Brazilian species.

2. Material and methods

2.1. Taxonomy and morphology

The morphological part of this study is based on specimens deposited in Coleção de História Natural da Universidade Federal do Piauí, Floriano (CHNUFPI); Centro de Coleções Taxonômicas da Universidade Federal de Minas Gerais, Belo Horizonte (UFMG); and Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany (ZFMK). Taxonomic descriptions follow the style of recent publications on Pholcidae (e.g., Huber et al. 2024a, b; based on Huber 2000). Measurements were done on a dissecting microscope with an ocular grid and are in mm unless otherwise noted; eye measurements are ± 5 µm. Photos were made with a Nikon Coolpix 995 digital camera (2048 × 1536 pixels) mounted on a Nikon SMZ 18 stereo microscope or a Leitz Dialux 20 compound microscope. CombineZP (https://combinezp.software.informer.com) was used for stacking photos. Drawings are partly based on photos that were traced on a light table and later improved under a dissecting microscope, or they were directly drawn with a Leitz Dialux 20 compound microscope using a drawing tube. Cleared epigyna were stained with chlorazol black. For scanning electron microscope (SEM) photos, specimens were dried in hexamethyldisilazane (HMDS) (Brown 1993), sputter-coated with gold, and photographed with a Zeiss Sigma 300 VP scanning electron microscope. The distribution map was generated with ArcMap 10.0.

2.2. Abbreviations

ALE – anterior lateral eye(s); ALS – anterior lateral spinneret(s); AME – anterior median eye(s); a.s.l. – above sea level; L/d – length/diameter; PME – posterior median eye(s); PMS – posterior median spinneret(s). Abbreviations used in figures only are explained in the figure legends.

2.3. Molecular phylogeny

2.3.1. Taxon sampling

To study the phylogenetic placement of the new Brazilian taxa, we sequenced both available species (three specimens) with a low coverage whole genome sequencing strategy. Since our original hypothesis was that these species might be related to the Chilean genus Aucana Huber, 2000 (for which no molecular data had been available), we analyzed four representatives of Aucana with the same method, and combined these new data with the ultra-conserved elements (UCEs) of 66 Pholcidae species from Meng et al. (2025). As outgroups, we used the same four taxa as in Meng et al. (2025).

2.3.2. Low coverage whole genome sequencing

Following the manufacturer’s instruction, DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) including the optional RNAse digest. DNA concentration and fragment size were determined using a QuantusTM Fluorometer (Cat # E6150, Promega Corporation, USA) and a Fragment Analyzer (Advanced Analytical Technologies, Inc.), respectively. Adapting parameters to the determined fragment size, DNA was fragmented by a Bioruptor® Pico sonication device (Diagenode S.A.). For each specimen, a total mass of 100 ng fragmented DNA was used for library construction with the NEBNext Ultra II FS DNA Library Prep Kit (NEB #7805), following the manufacturer’s instruction. During this process, the fragmented DNA was subject to end-repair, dA-tailing and ligation of molecular-barcoded adaptors, and purified with AMPure® XP Beads (Beckman Coulter, Inc. #A63881). The indexed libraries were then further amplified and purified. Finally, concentration and fragment size distributions of the DNA libraries were analyzed again and sequenced by a commercial company (Macrogen Europe) using pair-end (PE) 150 bp strategy. Each specimen was sequenced with ca. 11 Gb of data.

2.3.3. Sequence assembly and UCE extraction

We used the Shovill pipeline (ver. 1.1.0; Seemann 2017) with default parameters for raw data filtering and sequence assembly. Specifically, Trimmomatic (ver. 0.39; Bolger et al. 2014) was employed for quality trimming and adapter clipping (--trim), followed by contig assembly with SPAdes (ver. 4.0.0; Prjibelski et al. 2020). Following Meng et al. (2025), we applied the “all-blast-all” method to filter out potential cross-contaminations among samples (blast similarity ≥ 99% and alignment length ≥100 bp were subject to check) and extracted UCE sequences from the remaining assembly with Phyluce (ver. 1.7.1; Faircloth 2016). The extracted UCE sequences were aligned with MAFFT (ver. 7.475; Katoh and Standley 2013) (--adjustdirection –maxiterate 1000), and resulting alignments were trimmed using TrimAl (ver. 1.4.rev15; Capella-Gutierrez et al. 2009) (-automated 1). Finally, five data matrices (matrices 1–5) were created based on different taxon coverage (50, 60, 70 and 80%) and minimum alignment length (50 vs 150 bp) (Table S2).

2.3.4. Systematic bias assessment

To assess potential systematic biases, we conducted a likelihood mapping analysis (Strimmer and von Haeseler 1997) using IQ-TREE (ver. 2.2.0; Minh et al. 2020) and matrix 1 to evaluate the treelikeness of 100,000 randomly sampled quartets. We also tested the assumptions of stationarity and homogeneity, which are integral to most molecular evolutionary models, by performing symmetry tests in IQ-TREE (Naser-Khdour et al. 2019; Minh et al. 2020) (--symtest-only). To investigate potential violations of the assumption of no intra-locus recombination, we applied 3SEQ (ver. 1.8.0; Boni et al. 2007; Lam et al. 2018), with a pre-computed 3000 × 3000 × 3000 p-value table for the analysis. PhyloMAd (ver. 1.2; Duchêne et al. 2022) was used to assess substitutional saturation. Additionally, for each locus, we computed key features such as average GC content, GC content interquartile range, the number and proportion of missing data (gaps and Ns), the number and proportion of parsimony-informative sites, the length of the multiple sequence alignment (MSA), the number of taxa in the MSA, and created a saturation plot using custom scripts. Finally, we visualized the distributions of these features using density plots, along with a missing data distribution plot, generated with ggplot2 (ver. 3.3.6; Ginestet 2011) and R (ver. 4.2.0; R Core Team 2020).

2.3.5. Phylogenetic inference

To each data matrix, we applied both concatenation- and coalescence-based methods using IQ-TREE (the best-fit model was determined by ModelFinder (Kalyaanamoorthy et al. 2017)), RAxML-NG (ver. 1.1; Kozlov et al. 2019) (model: GTR+R4+I+FO), unweighted and weighted ASTRAL-IV (ver. 1.19.4.5; Zhang and Mirarab 2022), SVDquartets (Chifman and Kubatko 2014) as implemented in PAUP* (ver. 4a168; Swofford 2002), and PhyloBayes-MPI (ver. 1.8; Lartillot et al. 2013) (model: CAT-GTR), following the methods in Meng et al. (2025). By down-weighting quartets with low support, long terminal branches, or both, the weighted version of ASTRAL offers stronger theoretical guarantees and improved empirical performance compared to the unweighted version (Zhang and Mirarab 2022). The resulting trees were visualized with Figtree (ver. 1.44) (https://github.com/rambaut/figtree). Additionally, we used DiscoVista (Sayyari et al. 2018) to calculate the relative gene frequency support for different topologies. For each tree, we compared all the other trees against it, calculating the total number of congruent and incongruent branches. The tree with the highest number of supported branches was selected as the preferred topology and used as reference for comparisons and for further discussion.

3. Results

3.1. Low coverage whole genome sequencing

A total of 66.28 Gbp raw data was generated from the low coverage whole genome sequencing, with a range of 7.80 to 13.48 Gbp for each of the six samples (G-codes in Table S1). Combining our new data with those from Meng et al. (2025) and NCBI, we created five data matrices (matrices 1–5), with total locus numbers ranging from 40 to 139, total sites ranging from 9.5 to 30.5 Kbp and numbers of contigs ranging from 2,632 to 7,573 (Table S2). Most sequences in matrix 1 have a length of about 200 bp (ranging from 50 to 550 bp), and missing data account for less than 2.5% of the alignment length (Figs S1 and S2). Likelihood mapping analyses show that about 32% of the quartets are located at each of the three corners of a triangular graph, suggesting that our dataset has high information content with respect to phylogenetic analysis (Fig. S3). For only 10 out of 139 loci (7.2%), the assumptions of stationarity or homogeneity, or both, were rejected (SymPval < 0.001) (Table S3). The substitution saturation analysis showed that all loci are under low risk of saturation (Table S4). Intralocus recombination analysis identified only 45 recombinant sequences (0.6% of 7,573 sequences) across 40 of the 139 loci analyzed (28.8%). Only 15 sequences (0.2%) contained recombinant segments longer than 100 bp, suggesting that subsequent phylogenetic analyses were unlikely affected by the violation of the assumption of free intralocus recombination (Table S5).

The main phylogeny is shown in Figure 1. Analyses from different data matrices and tree construction methods mostly reconstructed the same subfamily-level topology as in Meng et al. (2025) and similar genus-level relationships, with Caipirinae subfam. nov. always being sister to ((Physocyclinae subfam. nov., Modisiminae), (Arteminae, Ninetinae)) in 26 of 30 analyses (Fig. 2A). The subfamily-level relationships have high gene frequency supports (≥ 41%) (Fig. 2B). In addition, the molecular data strongly reject our original hypothesis that the Chilean genus Aucana Huber, 2000 might be the closest relative of the two new Brazilian species described below. Instead, Aucana is resolved as the only South American genus of Physocyclinae subfam. nov.

Figure 1.

Maximum likelihood tree based on UCE (ultra-conserved elements) data. The tree was constructed with RAxML-NG and matrix 1 using a partitioned strategy and the GTR+R4+I+FO model. Circles on the nodes represent bootstrap support (BS) values, with green circles indicating strong support (BS: 95%–100%), orange circles moderate support (BS: 70%–95%), and red circles weak support (BS < 70%). Representatives of each subfamily on the right, from top: Hoplopholcus konya Huber, 2020; Apokayana kapit (Huber, 2016); Caipira mineira Huber sp. nov.; Artema martensi Huber, 2021; Ibotyporanga walekeru Huber, 2024; Arnapa arfak Huber, 2019; Mesabolivar eberhardi Huber, 2000; photos BAH.

Figure 2.

Subfamily-level phylogeny and supporting evidence. a Phylogenetic relationships among subfamilies. Branch panels display congruence (green) and incongruence (red) across different analyses based on data matrices (matrices 1–5) and various tree construction methods. Branch labels correspond to the subfigure headings in b. The primary topology is derived from Figure 1. b Relative gene frequency for alternative topologies. Subfigure titles and x-axis labels correspond to the branch labels in a. The subfamily-level phylogeny is supported by most analyses and the new subfamily Caipirinae is sister of ((Physocyclinae subfam. nov., Modisiminae), (Arteminae, Ninetinae)), with high gene frequency supports (41%).

3.2. Taxonomy

3.2.1. Subfamily Caipirinae subfam. nov.

In Family Pholcidae C.L. Koch, 1850

Type genus.

Caipira Huber gen. nov.

Diagnosis and Description.

See single known genus below.

Remarks.

Our genomic data resolve Caipira gen. nov. as sister to a large clade composed of four subfamilies (Fig. 1); the new genus can thus not be assigned to an existing subfamily. Morphologically, Caipirinae subfam. nov. cannot easily be distinguished from related subfamilies. The two known Caipira species remind of certain Ninetinae, Modisiminae, and Physocyclinae subfam. nov. (see genus diagnosis below) but the sister group of Caipirinae does not seem to be characterized by any morphological synapomorphy.

Composition.

Monogeneric.

3.2.2. Genus Caipira Huber, gen. nov.

https://zoobank.org/532DFFE5-EF60-4E09-88E7-C5CB36B226CF

Type species.

Caipira mineira Huber sp. nov.

Diagnosis.

Small Pholcidae (body size < 1.5 mm) with relatively short legs (tibia 1 L/d: 13–15) and globular abdomen (Fig. 3). Distinguished from representatives of superficially similar South American genera in Modisiminae, Ninetinae, and Physocyclinae subfam nov. (e.g., Arenita Huber & Carvalho, 2019; Aucana Huber, 2000; Blancoa Huber, 2000; Canaima Huber, 2000; Kairona Huber & Carvalho, 2019; Kambiwa Huber, 2000; Nerudia Huber, 2000; Tupigea Huber, 2000) by combination of: (1) carapace with pair of dark marks (Fig. 3); superficially similar Ninetinae lack such paired marks; (2) strong prolateral-ventral process on male palpal tarsus, at basis of procursus (arrows in Figs 6b, 16b); (3) prominent transversal ridge on male genital bulb, on prolateral-dorsal side (arrows in Figs 6d, e, 16d, e); (4) pair of pointed male cheliceral apophyses (Figs 7a, b, 17b, c) and corresponding pair of female epigynal pockets (Figs 7c, 17d); (5) absence of pseudosegmentation (Fig. 13e); (6) very low ratio of tibia 1 / tibia 2 (~1.05–1.15); higher in most other pholcids except some Ninetinae (Fig. 20). For further discussion of individual diagnostic traits, see Discussion.

Figure 3.

Live specimens. a, b Caipira mineira Huber sp. nov. from Gruta do Janelão; male and female with egg-sac. c, d Caipira baiana Huber sp. nov. from W of Queimada Nova; male and female with egg-sac.

Description.

Total body length ~1.1–1.4; carapace width 0.50–0.60. AME either present (C. mineira) or strongly reduced to absent (C. baiana). Legs relatively short: male tibia 1 length 0.8–1.1; female tibia 1 length: 0.7–1.0; male tibia 1 L/d: 13–15. Color (in ethanol) mostly whitish to pale ochre-yellow, with pair of darker ochre marks on carapace; sternum monochromous whitish; legs either without darker rings (C. mineira) or with rings on femora and tibiae (C. baiana); abdomen either monochromous (C. mineira) or with distinct white marks (C. baiana). Ocular area barely raised. Thoracic groove shallow (Fig. 9a, b). Male clypeus either unmodified (C. mineira) or with pair of short rounded processes near margin and many strong hairs directed upwards (C. baiana; Fig. 17a). Sternum wider than long, unmodified. Abdomen globular. ALS either with eight spigots each (C. mineira; Fig. 10b–e) or with only two spigots each (C. baiana; not studied with SEM; based on cleared female abdomen observed in compound microscope). Gonopore in C. mineira with four epiandrous spigots arranged in two pairs (arrows in Fig. 9f); not studied in C. baiana. Male chelicerae with pair of distal pointed apophyses directed towards median, and pair of proximal lateral sclerotized humps (Figs 7a, b, 17b, c); without stridulatory ridges (Fig. 9d). Male palps either with strongly widened femur (C. mineira; Fig. 5) or with much smaller femur with distinct prolateral-ventral sclerotized apophysis (C. baiana; arrow in Fig. 15a); condyles of tibia-tarsus joints either shifted towards prolateral (C. mineira) or towards retrolateral (C. baiana); tarsus with prolateral-ventral process at basis of procursus (arrows in Figs 6b, 16b); procursus distally with heavily sclerotized element with pointed tips (Figs 6a–c, 16a–c); genital bulb slightly elongated and medially constricted, with prolateral-dorsal protruding flap or ridge (arrows in Figs 6d, e, 16d, e), sperm duct opening distally on bulb (arrows in Fig. 11a, c). Legs without spines, without curved hairs. With sexually dimorphic short ‘vertical’ hairs on male tibia 1 only (Fig. 13a). Ventrally on metatarsi 3 and 4 with slender hairs (Fig. 12a–d) as described recently in Ninetinae and ‘other Arteminae’ (now Physocyclinae subfam. nov.) (Huber et al. 2023a, Huber et al. 2024b). Retrolateral trichobothria on leg tibiae in very distal position (male tibia 1: at ~50–60% of tibia length); prolateral trichobothrium absent on tibia 1, present on tibiae 2–4. No tarsal pseudosegmentation visible (also in SEM and in compound microscope). Tarsus 4 distally with two comb-hairs on prolateral side (arrows in Fig. 13f; studied in C. mineira only). Main and median tarsal claws as typical for family.

Etymology.

The genus name is derived from the traditional rural culture of Brazil; gender feminine.

Relationships.

See results of molecular analysis above.

Distribution.

Known from limestone outcrop terrains in the Irecê and Peruaçu biogeographic districts (sensu Moro et al. 2024) of the Caatinga domain, in the Brazilian states of Minas Gerais and Bahia (Fig. 4).

3.2.3. Caipira mineira Huber, sp. nov.

https://zoobank.org/6A1020F5-61CE-4769-BB6B-9F75AF0033B8

Figures 3a, b, 5–14

Material examined.

Holotype: BRAZIL - Minas Gerais • ♂; Parque Nacional Cavernas do Peruaçu, Gruta do Janelão, ~100–300 m from cave entrance; ~15.125°S, 44.240°W (coordinates: cave entrance); ~600 m a.s.l.; 14 Nov. 2022; B.A. Huber, L.S. Carvalho & R.A. Torres leg.; CHNUFPI 9069. — Paratypes: BRAZIL - Minas Gerais • 2 ♂♂, 2 ♀♀; same collection data as for holotype; CHNUFPI 9070 • 1 ♂, 1 ♀; same collection data as for holotype; UFMG 33242 • 4 ♂♂, 4 ♀♀, and one female abdomen (cleared and transferred from ZFMK Br22-166); same collection data as for holotype; CHNUFPI 9071 [deposited in ZFMK Ar 24704] • 1 ♀; same collection data as for holotype; CHNUFPI 9072 • 2 ♂♂, 2 ♀♀, 3 juvs.; same locality as for holotype, “PNCP15”; 29 Feb. 2020; A.J. Santos et al. leg.; CHNUFPI 4193. — Other material examined. BRAZIL - Minas Gerais • 1 ♂, 5 ♀♀, in pure ethanol; same collection data as for holotype; CHNUFPI 9073 [deposited in ZFMK Br22-166] (vouchers for UH485, G48; 1 ♂ and 1 ♀ used for SEM; one female abdomen cleared and transferred to ZFMK Ar 24704) • 1 ♂, in pure ethanol; same locality as holotype, “PNCP16”; 1 Mar. 2020; A.J. Santos et al. leg.; CHNUFPI 3505 (voucher for E073) • 2 ♂♂, 1 ♀; Parque Nacional Cavernas do Peruaçu, Lapa do Rezar (karst cave, at cave entrance); 15.1433°S, 44.2349°W; 610 m a.s.l.; 14 Nov. 2022; B.A. Huber, L.S. Carvalho & R.A. Torres leg.; CHNUFPI 9074 [deposited in ZFMK Ar 24705] • 3 juvs, in pure ethanol; same collection data as for preceding; CHNUFPI 9075 [deposited in ZFMK Br22-169] (voucher for UH057).

Diagnosis.

Easily distinguished from C. baiana Huber sp. nov. by much wider male palpal femur without ventral apophysis (compare Figs 5 and 15) and by smaller distances between male cheliceral apophyses and between female epigynal pockets (compare Figs 7 and 17). From all other known Pholcidae by shape of procursus (Figs 6a–c, 11; slender, proximally with ventral notch and ventral process, distally with dorsal rounded sclerite and ventral membranous hooked element); also by shape of genital bulb (Figs 6d–f, 11a–e; dorsal protruding flap; distal pointed sclerite), by armature of male chelicerae (Figs 7a, b, 9c, d; pair of lateral sclerotized humps and pair of frontal pointed apophyses directed towards median), and by female epigynum and internal genitalia (Figs 7c, d, 8; anterior plate with pair of pockets close together; posterior plate anteriorly with pair of dark marks; internal genitalia with complex and large median rounded sclerotized structure); from most Pholcidae also by combination of large male palpal femur (Fig. 5; much larger than tibia) and small size (body length ~1.2 mm; prosoma width ~0.5 mm).

Description.

MALE (holotype). Measurements: Total length 1.20, carapace width 0.50. Distance PME–PME 30 µm; diameter PME 45 µm; distance PME–ALE 10 µm; diameter AME 20 µm; distance AME–AME 10 µm. Leg 1: 3.23 (0.93 + 0.17 + 0.90 + 0.83 + 0.40), tibia 2: 0.80, tibia 3: 0.70, tibia 4: 0.98; tibia 1 L/d: 15. — Color (in ethanol): Carapace whitish with pair of lateral submarginal ochre bands, clypeus ochre; sternum white; legs pale ochre-yellow, without dark rings; abdomen monochromous ochre gray. — Body: Habitus as in Fig. 3a. Ocular area barely raised. Thoracic groove shallow (Fig. 9a). Clypeus unmodified. Sternum wider than long (0.40/0.30), unmodified. Abdomen globular. ALS with one strongly widened spigot, one long pointed spigot, and apparently six cylindrical spigots (Fig. 10b). PMS with two slender spigots (cf. Fig. 10f). Gonopore with four epiandrous spigots arranged in two pairs (Fig. 9f). — Chelicerae: As in Fig. 7a, b, with pair of frontal pointed apophyses directed towards median, without modified hairs (Fig. 9c, d), and pair of lateral sclerotized humps with series of frontal ridges (Fig. 9d), without lateral stridulatory ridges. — Palps: As in Figs 5 and 11; coxa unmodified; trochanter with short ventral apophysis (~25 µm long); femur large and strongly widened, dorsally bulging, without stridulatory pick; femur-patella condyles shifted toward prolateral side; tibia with two trichobothria in very proximal position; tibia-tarsus condyles slightly shifted toward prolateral side; tarsus with strong prolateral-ventral process and deep notch ventrally at basis of procursus (Fig. 6b); tarsal organ exposed (Fig. 14a), diameter ~10 µm; procursus (Fig. 6a–c) slender, proximally with ventral process, distally with dorsal rounded sclerite and ventral membranous hooked element (Fig. 11f); genital bulb (Fig. 6d–f) slightly elongated, with distinctive dorsal protruding flap and distal pointed sclerite, sperm duct opening distally on bulb (arrows in Fig. 11a, c). — Legs: Without spines, without curved hairs. Tibiae, metatarsi, and tarsi with round cuticular ‘plates’ (Figs 12a, 13c) at regular intervals, diameter ~4–5 µm. Without rimmed pores. With sexually dimorphic short ‘vertical’ hairs (Fig. 13a) on tibia 1 only, diameter proximally 1.4 µm, length ~15–20 µm; putative chemoreceptors on all legs, especially distally, i.e. on metatarsi and tarsi, similar to sexually dimorphic short ‘vertical’ hairs but with several side branches (Fig. 13b) and slightly thicker (diameter proximally 1.6 µm). Ventrally on metatarsi 3 and 4 with slender hairs (Fig. 12a–d); diameters proximally 1.6 µm, versus 2.8 µm in neighboring mechanoreceptors; shape of hair basis similar to neighboring mechanoreceptors (Fig. 12c), but shaft similar to trichobothria (cf. Fig. 12e–f); metatarsus 3 with only three such hairs, metatarsus 4 with ~14; distally very thin and long, with distinctively widened tips (Fig. 12d; ~1.4 µm diameter, versus 0.6 µm subdistally). Bases of trichobothria capsulate, unmodified (Fig. 12e, f); trichobothria feathered (Fig. 12e, f); retrolateral trichobothrium of tibia 1 at 48%; prolateral trichobothrium absent on tibia 1. No tarsal pseudosegmentation visible in SEM (Fig. 13e) and in compound microscope. Leg tarsal organs exposed (Fig. 14f), diameters ~3–6 µm. Main and median tarsal claws as typical for family; main claws with 9–10 tines (Fig. 13d–f). Tarsus 4 distally with two comb-hairs on prolateral side (Fig. 13f).

Variation.

MALE. Tibia 1 in 13 males (incl. holotype): 0.90–1.07 (mean 0.97).

Description.

FEMALE. In general very similar to male, including size and carapace pattern (Fig. 3b). Chelicerae also without stridulatory ridges (Fig. 9e). Tibia 1 in 14 females: 0.83–0.93 (mean 0.89). With short chemoreceptive hairs like in male but without sexually dimorphic short ‘vertical’ hairs. Spinnerets as in male (Fig. 10c–f). Palpal tibia with only one trichobothrium (Fig. 12e). Epigynum (Fig. 8a, b) anterior plate light brown, strongly indented posteriorly, with pair of pockets close together near posterior margin (Fig. 7c); posterior epigynal plate large but simple, with pair of darker marks anteriorly (muscle attachment sites?). Internal genitalia partly visible in uncleared specimens; with sclerotized roundish median structure from which pair of lateral sclerites originate; pore plates poorly visible, apparently at median origin of lateral sclerites (Fig. 7d); with large anterior membranous arc.

Etymology.

The species name is an adjective, describing someone originating from Minas Gerais state, Brazil.

Distribution.

Known from two caves (~2 km from each other) in Parque Nacional Cavernas do Peruaçu, Minas Gerais state, Brazil (Fig. 4).

Figure 4.

Known geographic distribution of Caipira gen. nov., including Caipira baiana Huber sp. nov. (red square) and Caipira mineira Huber sp. nov. (green circle). Colored areas represent the main districts of the Caatinga domain sensu Moro et al. (2024): CDI – Chapada Diamantina; IRE – Irecê; PER – Peruaçu; SDS – Southern Depressão Sertaneja; and SFD – São Francisco Dunes. Other biomes are not shown. Note: Peruaçu and Irecê districts are the only limestone outcrop terrains in this region, separated by the crystalline terrains of the Southern Depressão Sertaneja and the Chapada Diamantina.

Natural history.

Both sites are karstic caves, located in the Peruaçu district of the Caatinga domain (sensu Moro et al. 2024). At the type locality, Gruta do Janelão (Fig. 19a), all specimens were found in the aphotic zone, ~100–300 m from the cave entrance. Measurements of temperature and humidity at approximately the same section of the cave: 24°C, 91% (A.J. Santos, 1 Mar. 2020). Searches carried out in Feb. 2020 and in Nov. 2022 explored about 700 of the 4,800 m extension of the cave, but no specimens were found in the twilight section and deeper in the cave. At the second locality, Lapa do Rezar, the specimens were found at the cave entrance. At both localities, the spiders were found under stones or among small limestone pebbles on the floor. Two egg sacs contained six and seven eggs, respectively, with an egg diameter of 0.40.

3.2.4. Caipira baiana Huber, sp. nov.

https://zoobank.org/59FE9223-CA80-4281-9B73-A5F43E67E7DE

Figures 3c–d, 15–18

Material examined.

Holotype: BRAZIL - Bahia • ♂; W of Queimada Nova; 11.0343°S, 42.0682°W; 580 m a.s.l.; 25 Nov. 2022; B.A. Huber & A.S. Michelotto leg.; CHNUFPI 9076. — Paratypes: BRAZIL - Bahia • 1 ♂, 1 ♀; same collection data as for holotype; CHNUFPI 9077 • 1 ♂ (together with one female abdomen, dissected and epigynum cleared, transferred from ZFMK Br22-229; voucher for G58); same collection data as for holotype; CHNUFPI 9078 [deposited in ZFMK Ar 24706]. — Other material examined: BRAZIL - Bahia • 1 ♂, 3 ♀♀ (one female prosoma used for molecular work; abdomen transferred to ZFMK Ar 24706), in pure ethanol; same collection data as holotype; CHNUFPI 9079 [deposited in ZFMK Br22-229; voucher for UH501].

Diagnosis.

Easily distinguished from C. mineira Huber sp. nov. by much slenderer male palpal femur with ventral apophysis (compare Figs 5 and 15) and by larger distances between male cheliceral apophyses and between female epigynal pockets (compare Figs 7 and 17). From all other known Pholcidae by shape of procursus (Fig. 16a–c; slender, distally with heavily sclerotized element with pointed tip); also by strong apophysis prolateral-ventrally on male palpal femur (arrow in Fig. 15a), by shape of genital bulb (Fig. 16d–f; prolateral-dorsal protruding flap; dorsal ridges), by armature of male chelicerae (Fig. 17a–c; pair of lateral sclerotized humps and pair of distal lateral pointed apophyses directed towards median), by pair of rounded processes on male clypeus (Fig. 17a), and by female epigynum and internal genitalia (Figs 17d, e, 18; main anterior plate with pair of pockets and additional pair of frontal lateral sclerotized areas; internal genitalia with arched element and pair of small elongated pore plates).

Figure 5.

Caipira mineira Huber sp. nov.; male from Gruta do Janelão; ZFMK Ar 24704. Left genital palp, prolateral (a), dorsal (b), and retrolateral (c) views. Scale bar: 0.2 mm.

Figure 6.

Caipira mineira Huber sp. nov.; male from Gruta do Janelão; CHNUFPI 3505. a–c Left tarsus and procursus, prolateral, dorsal, and retrolateral views; arrow: prolateral-ventral process. d–f Left genital bulb, prolateral, dorsal, and retrolateral views; arrows: prolateral-dorsal ridge. Scale bars: 0.2 mm.

Figure 7.

Caipira mineira Huber sp. nov.; male and female from Gruta do Janelão; CHNUFPI 3505 (male), ZFMK Ar 24704 (female). a, b Male chelicerae, frontal and lateral views. c, d Cleared female genitalia in ventral (external) and dorsal (internal) views. Abbreviations: ca, cheliceral apophysis; ep, epigynal pocket; pp, pore plate. Scale bars: 0.2 mm.

Figure 8.

Caipira mineira Huber sp. nov.; two females from Gruta do Janelão; ZFMK Ar 24704. a, b Epigyna, ventral views. c, d Cleared female genitalia of female shown in a, ventral and dorsal views. e, f Cleared female genitalia of female shown in b, ventral and dorsal views. Scale bars: 0.2 mm.

Figure 9.

Caipira mineira Huber sp. nov.; male and female from Gruta do Janelão; ZFMK Br22-166. a Male prosoma, frontal view. b Female prosoma, frontal view. c Right male frontal cheliceral apophysis, frontal view. d Right male chelicera, frontal-lateral view. e Right female palp and chelicera, frontal-lateral view. f Male gonopore and epiandrous spigots (arrows), ventral view. Scale bars: 100 µm (a, b), 10 µm (c, d, f), 20 µm (e).

Figure 10.

Caipira mineira Huber sp. nov.; male and female from Gruta do Janelão; ZFMK Br22-166. a Epigynum, ventral view, showing pockets (arrows). b Male anterior lateral spinnerets (ALS) and posterior median spinnerets (PMS). c–e Female ALS and PMS. f Female PMS. Scale bars: 100 µm (a), 10 µm (b–e), 2 µm (f).

Figure 11.

Caipira mineira Huber sp. nov.; male from Gruta do Janelão; ZFMK Br22-166. a Right palp, retrolateral view. b Left palp prolateral view. c Right palp, retrolateral-dorsal view. c Left palp, prolateral-dorsal view. e Left palp, dorsal view. f Tip of right procursus, retrolateral view. Arrows in a and c point at sperm duct opening. Abbreviations: b, genital bulb; f, femur; pa, patella; pr, procursus; ta, tarsus; ti, tibia; tr, trochanter. Scale bars: 100 µm (a–e), 20 µm (f).

Figure 12.

Caipira mineira Huber sp. nov.; male and female from Gruta do Janelão; ZFMK Br22-166. a Right female metatarsus 4, showing similarity of trichobothrium (t) and slender metatarsal hair (arrow). b Left male metatarsus 3, prolateral view, showing three slender metatarsal hairs (arrows). c Right female metatarsus 4, bases of regular mechanoreceptor and of slender metatarsal hair (arrow). d Tip of slender metatarsal hair on left male metatarsus 3. e Female palpal tibia, showing single trichobothrium. f Prolateral trichobothrium on left male tibia 3. Scale bars: 10 µm (a, b, e, f), 3 µm (c), 2 µm (d).

Figure 13.

Caipira mineira Huber sp. nov.; male from Gruta do Janelão; ZFMK Br22-166. a Sexually dimorphic short ‘vertical’ hair (arrow) on left tibia 1. b Putative chemoreceptor on left metatarsus 1. c Round cuticular plate (arrow) on right tarsus 4. d Tip of left tarsus 1, prolateral view. e Left tarsus 3, prolateral-distal view. f Tip of left tarsus 4, prolateral view, showing two comb hairs (arrows). Scale bars: 10 µm (a, d–f), 1 µm (b), 2 µm (c).

Figure 14.

Caipira mineira Huber sp. nov.; male and female from Gruta do Janelão; ZFMK Br22-166. a Tarsal organ (arrow) and neighboring sensilla on right male palp. b Tip of right female palp, dorsal view, showing tarsal organ (arrow). c–f Tarsal organs on right female tarsus 1 (c), right female tarsus 2 (e), right female tarsus 3 (e), and right male tarsus 4 (f). Scale bars: 2 µm (a, c–f), 10 µm (b).

Description.

MALE (holotype). Measurements: Total length 1.30, carapace width 0.58. Distance PME–PME 40 µm; diameter PME 60 µm; distance PME–ALE 15 µm; AME absent (no lenses, only black mark). Leg 1: 3.22 (0.88 + 0.20 + 0.88 + 0.88 + 0.38), tibia 2: 0.84, tibia 3: 0.64, tibia 4: 0.84; tibia 1 L/d: 13. — Color (in ethanol): Prosoma and legs mostly whitish to pale ochre-yellow, carapace with pair of ochre marks beside ocular area, clypeus also slightly darkened; sternum monochromous whitish; legs with darker rings on femora (subdistally) and tibiae (proximally and subdistally); abdomen ochre gray, with distinct white marks except on ventral side. — Body: Habitus as in Fig. 3c. Ocular area barely raised. Thoracic groove shallow. Clypeus with pair of short rounded processes near margin and many strong hairs directed upwards (Fig. 17a). Sternum wider than long (0.38/0.34), unmodified. Abdomen globular. — Chelicerae: As in Fig. 17a–c, with pair of distal lateral pointed apophyses directed towards median, and pair of proximal lateral sclerotized humps; without stridulatory ridges. — Palps: As in Fig. 15; coxa with low ventral hump; trochanter unmodified; femur relatively small (smaller than tibia), with strong prolateral-ventral sclerotized apophysis (arrow in Fig. 15a), distally strongly widened; femur-patella condyles not shifted to one side; tibia with two trichobothria; tibia-tarsus condyles strongly shifted toward retrolateral side; tarsus with prolateral-ventral process at basis of procursus; procursus (Fig. 16a–c) proximally simple, distally with heavily sclerotized element with pointed tip; genital bulb (Fig. 16d–f) slightly elongated and medially constricted, with distinctive prolateral-dorsal protruding flap and dorsal ridges, sperm duct opening not seen (presumably on distal membranous part). — Legs: Without spines, without curved hairs. With sexually dimorphic short ‘vertical’ hairs on tibia 1 only (confirmed in compound microscope; not visible in dissecting microscope). Ventrally on metatarsi 3 and 4 with slender hairs (confirmed in compound microscope; not visible in dissecting microscope). Retrolateral trichobothrium of tibia 1 at 61%; prolateral trichobothrium absent on tibia 1. No tarsal pseudosegmentation visible (also in compound microscope). Main tarsal claws and median tarsal claw as typical for family.

Figure 15.

Caipira baiana Huber sp. nov.; male from W of Queimada Nova; ZFMK Ar 24706. Left genital palp, prolateral (a), dorsal (b), and retrolateral (c) views; arrow: sclerotized apophysis on femur. Scale bar: 0.2 mm.

Figure 16.

Caipira baiana Huber sp. nov.; male from W of Queimada Nova; ZFMK Ar 24706. a–c Left tarsus and procursus, prolateral, dorsal, and retrolateral views; arrow: process at basis of procursus. d–f Left genital bulb, prolateral, dorsal, and retrolateral views; arrows: prolateral-dorsal ridge. Scale bars: 0.1 mm.

Figure 17.

Caipira baiana Huber sp. nov.; male and female from W of Queimada Nova; ZFMK Ar 24706. a Male ocular area, clypeus, and chelicerae, oblique frontal view. b, c Male chelicerae, frontal and lateral views. d, e Cleared female genitalia, ventral and dorsal views. Abbreviations: ca, cheliceral apophysis; ep, epigynal pocket; pp, pore plate. Scale bars: 0.2 mm.

Figure 18.

Caipira baiana Huber sp. nov.; female from W of Queimada Nova; ZFMK Ar 24706. a, b Abdomen ventral view, and epigynum at higher magnification. c, d Cleared female genitalia, ventral and dorsal views. Scale bars: 0.2 mm.

Figure 19.

Type localities of newly described species. a Gruta do Janelão, entrance area; Caipira mineira Huber sp. nov. was found ~100–300 m from the cave entrance, in the aphotic zone. b Thorny woodland W of Queimada Nova; Caipira baiana Huber sp. nov. was found in the collapsed rock wall visible in the left central part of the photo. Photos BAH.

Figure 20.

a Ratio of male tibia 1 / male tibia 2 in 1662 species (x-axis) of Pholcidae, taken from the taxonomic literature and sorted in each subfamily from smallest to largest values (Art. = Arteminae; Cai. = Caipirinae subfam. nov.; Mod. = Modisiminae; Nin. = Ninetinae; Pho. = Pholcinae; Phy. = Physocyclinae subfam. nov.; Sme. = Smeringopinae). Note that the values for the two new species of Caipirinae subfam. nov. described herein are among the lowest known in Pholcidae. b Scatter plot of the ratio male tibia 1 / male tibia 2 on a proxy of male leg length (tibia 1 length). Note that the lower left corner of the plot is almost entirely filled by Ninetinae and Caipirinae subfam. nov. Erroneous and dubious measurements reported in the literature were excluded (Table S6).

Variation.

MALE. Tibia 1 in three other males: 0.82, 0.82, 0.84.

Description.

FEMALE. In general, very similar to male (size, body shape, color pattern; Fig. 3d), but clypeus unmodified and legs without sexually dimorphic short ‘vertical’ hairs. One female with tiny AME lenses (diameter ~5 µm). Palpal tibia with two trichobothria. Tibia 1 in three females: 0.70, 0.72, 0.82. Epigynum (Fig. 18a, b) anterior plate wide and short, with pair of pockets and additional pair of frontal lateral sclerotized areas; posterior epigynal plate very short, indistinct. Internal genitalia (Figs 17e, 18c, d) with strong arched element (visible in uncleared specimens) and pair of small, elongated pore plates.

Etymology.

The species name is an adjective, describing someone originating from Bahia state, Brazil.

Distribution.

Known from type locality only, in Bahia state, Brazil (Fig. 4).

Natural history.

The type-locality is in the Irecê district of the Caatinga domain (sensu Moro et al. 2024). All specimens were found in an old collapsed low stone fence in thorny woodland (Fig. 19b). They shared this microhabitat with three further species of Pholcidae: Ibotyporanga diroa Huber & Brescovit, 2003; an undescribed species of Mesabolivar González-Sponga, 1998; and an undescribed species tentatively assigned to Tupigea Huber, 2000. One egg sac contained eleven eggs; egg diameter 0.38–0.39.

3.2.5. Subfamily Physocyclinae subfam. nov.

In Family Pholcidae C.L. Koch, 1850

Type genus.

Physocyclus Simon, 1893

Remarks.

Recent multi-locus genetic data (Eberle et al. 2018) suggested that Arteminae as previously defined (Huber 2011b) is polyphyletic: Artema and ‘other Arteminae’ are not sister taxa. This result is strongly supported by new genomic data (Meng et al. 2025; and herein), emphasizing the need for a new name for ‘other Arteminae’. Since no subfamily-level name for this group is available in the literature, we chose Physocyclus Simon, 1893 as the type genus of the new subfamily Physocyclinae. This subfamily includes all Arteminae as listed in the recent literature (Huber 2011b; Huber et al. 2018; Huber et al. 2024b) except for Artema. We also include here Aucana Huber, 2000 because our new genomic data strongly supports this assignment. Since the subfamily is based on molecular data and includes a range of morphologically diverse genera, we consider the diagnosis below of rather limited practical value. We provide the diagnosis because ICZN Article 13.1. could be interpreted as requiring such a diagnosis.

Diagnosis.

Small to medium-sized pholcids (carapace width 0.4–2.8), usually with relatively long legs (tibia 1 / carapace width usually > 3; shorter in Aucana Huber, 2000; Changminia Yao and Li, 2022; Nita Huber and El Hennawy, 2007; and in most species of Chisosa Huber, 2000), usually with eight eyes (AME very rarely absent, e.g. in Pholcitrichocyclus watta (Huber, 2001)). Distinguished from most other subfamilies by the combination of (1) presence of cheliceral stridulation (absent in Caipirinae subfam. nov., Modisiminae, Priscula Simon, 1893; most Pholcinae, southern clade of Smeringopinae; present in Artema Walckenaer 1837; Ninetinae; northern clade of Smeringopinae) and (2) strongly widened femur of male palp (similar in Artema, Priscula; certain species of Mesabolivar González-Sponga, 1998); Artema is distinguished from Physocyclinae by series of unique conical setae on male chelicerae (never present in Physocyclinae). Caipirinae is further distinguished from Physocyclinae by pair of epigynal pockets (never present in Physocyclinae).

Composition.

The subfamily as circumscribed here currently includes 107 nominal species in the following 11 genera (species numbers in parentheses): Arnapa Huber, 2019 (6); Aucana Huber, 2000 (5); Changminia Yao and Li, 2022 (2); Chisosa Huber, 2000 (4); Holocneminus Berland, 1942 (3); Nita Huber and El Hennawy, 2007 (1); Pholcitrichocyclus Ceccolini and Cianferoni, 2022 (= Trichocyclus Simon, 1908) (23); Physocyclus Simon 1893 (39); Serratochorus Wunderlich, 1988 (1); Tibetia Zhang, Zhu and Song, 2006 (1); Wugigarra Huber, 2001 (22).

4. Discussion

4.1. How reliable is the molecular phylogeny?

In our likelihood mapping analysis, approximately 32% of quartets are positioned at each of the three corners of the triangular graph, indicating a high level of phylogenetic signal in the dataset and the potential to resolve a robust phylogeny (Strimmer and von Haeseler 1997) (Fig. S3). Only 7.2% of the loci violate the assumptions of stationarity, homogeneity, or both (Table S3), and less than 0.6% of the contigs are affected by intra-locus recombination (Table S5). This suggests that the dataset is well-suited for phylogenetic inference. Furthermore, the coalescence-based methods (ASTRAL-IV and wASTRAL) enable us to mitigate the impact of incomplete lineage sorting (ILS) (Zhang and Mirarab 2022). The models GTR+R4+I+FO used in RaxML-NG and CAT-GTR in PhyloBayes-MPI are designed for handling rate and compositional heterogeneity (Lartillot et al. 2013; Kozlov et al. 2019), which alleviates potential influences of model violation.

Our phylogenetic inferences from 30 different analyses (five matrices × six tree construction methods) are largely congruent in terms of subfamily monophylies and inter-subfamily relationships (375 green squares / (30 × 13 panels) = 96%; see Fig. 2a). The monophylies of Pholcinae, Smeringopinae, Modisiminae, Ninetinae, Physocyclinae subfam. nov., and Arteminae appear beyond doubt. The monophyly of the new subfamily Caipirinae is supported by all analytical methods in our study (Fig. 2a) with 100% bootstrap support (Fig. 1). Non-monophyly of subfamilies was found in only a few analyses: (1) Arteminae, when analyzed with PhyloBayes-MPI using data matrices 3–5 (3 out of 30 analyses), which may be due to an insufficient amount of data (total sites ranging from 9 to 20 Kbp), and (2) Modisiminae, when analyzed with SVDquartets using matrices 1–5. The latter case involves the uncertain placement of three genera (Arenita and two unnamed genera). In most analyses (25 out of 30 analyses), they were sister to all other Modisiminae (Fig. 1), while in a few cases (5 out of 30 analyses) they were sister to Physocyclinae subfam. nov. (not shown), suggesting that further analysis of this poorly known group is necessary. The inconsistency between SVDquartets and other programs could stem from the fact that finding the species tree with maximum quartet support from a set of quartet trees is an NP-hard problem (Jiang et al. 2001). As SVDquartets uses a heuristic search strategy, it does not guarantee to find the optimal solution (Vachaspati and Warnow 2018).

Since a large percentage of our dataset is identical to that analyzed in Meng et al. (2025), it is unsurprising that the subfamily relationships recovered herein align well with those reported in Meng et al. (2025). Only a small fraction of the analyses (7 out of 90) did not support the monophyly of certain higher-level groups (Fig. 2a): (1) the clade ((Arteminae, Ninetinae), (Physocyclinae, Modisiminae)); (2) its sister-group relationship with the newly proposed subfamily Caipirinae; and (3) the entire family Pholcidae. Interestingly, all of these discrepancies arose from analyses based on the smaller datasets of matrices 4 and 5 (total sites: 15 Kbp and 9 Kbp, respectively). This suggests that the incongruences are likely due to the limited data in these specific matrices. Finally, although sparse taxon sampling can compromise phylogenetic inference, denser sampling – even when using short marker genes – has been shown to improve accuracy (Nichols et al. 2015; Kulkarni et al. 2023). In this context, Meng et al. (2025) analyzed combined genomic-scale data and six short marker genes for more than 900 pholcid species and recovered subfamily-level relationships congruent with our results.

4.2. Morphological aspects

The sister-group relationship between the two newly described species is strongly supported by molecular data but not immediately obvious in their morphology. The combined similarities listed in the diagnosis of the genus appear suitable for the particular purpose of differentiation from other genera, but rather weak in the context of phylogeny. Individually, most of these characters or traits do not seem to be unique among Pholcidae, i.e. they are unlikely candidates to be non-homoplastic synapomorphies. A possible exception is the transversal ridge on the male genital bulb (Figs 6d, e, 16d, e). For all other items listed in the diagnosis, similar characters and traits occur in other, often distantly related, genera. (1) Pointed male cheliceral apophyses and a corresponding pair of female epigynal pockets also occur in other genera like Belisana Thorell, 1898; Crossopriza Simon, 1893; Quamtana Huber, 2003; and Smeringopus Simon, 1890 (Huber 2003, 2005, 2012, 2022) but are absent in the sister group of Caipira gen. nov., i.e. in Physocyclinae subfam. nov., Modisiminae, Arteminae, and Ninetinae. (2) A ventral or prolateral process on the male palpal tarsus, at the basis of procursus, exists in many Pholcidae, even though usually less distinct, as for example in Crossopriza, Smeringopina Kraus, 1957 and Wanniyala Huber and Benjamin, 2005 (Huber 2013, 2019, 2022). (3) Dark marks on the carapace are ubiquitous in Pholcidae and only useful as a quick distinguishing trait in comparison to superficially similar Brazilian Ninetinae. (4) A low ratio of male tibia 1 / tibia 2 (~1.05–1.15) is very rare among Pholcidae (Fig. 20), but similar values also occur in Ninetinae. (5) The absence of leg tarsal pseudosegmentation is difficult to evaluate since the pseudosegmentation of some Pholcidae is very indistinct, or the individual pseudosegments are ‘broken’ into many seemingly irregular small platelets (in some Smeringopinae and some Physocyclinae subfam. nov.; Huber 2000, 2022).

On the other hand, the two species show some remarkable differences that are unusual among closely related and congeneric Pholcidae. The male palpal femur is particularly different: strongly enlarged in Caipira mineira (very similar to most Physocyclinae subfam. nov., also Artema, some Priscula, some Mesabolivar; e.g. Aharon et al. 2017; Huber 2018; Huber & Villarreal 2020) but much smaller and with strong ventral process in C. baiana (ventral apophyses are common in some Modisiminae genera and usually relatively conserved among close relatives; e.g. Huber 2000). Noteworthy is also the different number of ALS spigots: Caipira mineira has the plesiomorphic set of eight spigots; C. baiana has the reduced set of only two spigots. A reduction of spigots has occurred repeatedly in Pholcidae, even though rarely within genera, e.g., in Belisana; Metagonia Simon, 1893; Pholcus Walckenaer, 1805; and Smeringopus (Huber 2000; 2005, 2011a, 2012). Male clypeus modifications have also evolved repeatedly in Pholcidae, sometimes within genera (Huber 2021), and are present in C. baiana but absent in C. mineira. Finally, the AME have been reduced repeatedly in Pholcidae, sometimes even within genera, as in Leptopholcus Simon, 1893; Mecolaesthus Simon, 1893; Modisimus Simon, 1893; Panjange Deeleman-Reinhold & Deeleman, 1983; Pholcus, Priscula, and Quamtana (Huber 2003, 2011a; Huber & Villarreal 2020); their presence in C. mineira but absence in C. baiana just adds one more reduction to the list. In sum, the discovery of further species may well justify a future split of Caipira into two genera, but currently we see no need and no justification to do so.

4.3. Notes on the biogeography of Caipirinae

The distribution of Caipirinae subfam. nov. is restricted to limestone outcrop terrains in northeastern Brazil (Fig. 4). Each described species is recorded from a single biogeographic district of the Caatinga domain, separated by over 500 km. While C. mineira sp. nov. was collected in the Peruaçu district, C. baiana sp. nov. was collected in the Irecê district (sensu Moro et al. 2024). These karstic districts are separated by the crystalline terrains of the Southern Depressão Sertaneja district (SDS in Fig. 4) and the Chapada Diamantina subprovince (CPD in Fig. 4). Pholcidae sampling in this region is sparse (see Fig. S4) and it is thus likely that other species or additional occurrences of the described species will be found in future focused campaigns. Likewise, the existence of a third limestone outcrop district in the Caatinga domain (i.e., the Potiguar district; see Moro et al. 2024) raises the possibility of additional Caipirinae taxa further north. It is worth noting that targeted pholcid sampling is fundamental to reduce this sampling bias, as previously demonstrated for Ninetinae taxa (see Huber et al. 2023b, 2024a).

As sister-group to a large lineage of Pholcidae hypothesized to have originated during the Cretaceous period (Meng et al. 2025), Caipirinae subfam. nov. appears to be a relict taxon, as previously reported for other organisms in the Peruaçu district. A striking example is Relictopiolus galadriel Pérez-González, Monte and Bichuette, 2017, a troglobitic Kimulidae harvestman from another cave of the Parque Nacional Cavernas do Peruaçu (Pérez-González et al. 2017), the type-locality of C. baiana. Relictopiolus galadriel diverged from its epigean sister-taxon Tegipiolus pachypus Roewer, 1949 about 40 Mya, during the Eocene, corroborating the hypothesis of an ancient divergence between relictual taxa from this region and their sister-taxa (Pérez-González et al. 2017). These two species are the only currently known kimulids from eastern Brazil, with the remaining species recorded from northern South America and Central America (Pérez-González et al. 2017). The Peruaçu district also harbors several other troglobites, including other harvestmen, whip-spiders, pseudoscorpions, isopods, amphipods, crickets, heteropterans, centipedes, and fish (Pérez-González et al. 2017; Polhemus and Ferreira 2018; Monte and Bichuette 2020; Ázara et al. 2020; Cardoso et al. 2021). Furthermore, the richest hotspot of subterranean biodiversity in South America (i.e., the Água Clara cave system; see Ferreira et al. 2023), is in the Peruaçu district.

The floristic composition of the Peruaçu district is well-studied and distinct from the Caatinga sensu stricto and sandy Caatinga of other regions in the Caatinga domains, thus forming a particular sub-type of Caatinga, called ‘arboreal Caatinga’ (Moro et al. 2024). Conversely, the flora of the Irecê district is the least studied karstic region in the Caatinga domain (Moro et al. 2024). Both districts share the high abundance of caves, with several troglobites described for the Irecê district too, including other pholcids (Machado et al. 2011), as well as scorpions (Esposito et al. 2017), isopods (Cardoso et al. 2022), amphipods (Bueno et al. 2022), beetles (Gnaspini et al. 1997) and catfishes (Bockmann and Castro 2010). The Pholcidae species Metagonia diamantina Machado, Ferreira & Brescovit, 2011, described from the Irecê district (Ferreira et al. 2011), also represents a relict taxon. This species belongs to the potiguar species-group whose representatives are typically found in low primary productivity environments such as caves and high-altitude regions (Huber et al. 2022). This distribution suggests that species of the potiguar group of Metagonia may have been replaced by modern taxa in more favorable environments (Huber et al. 2022).

These abundant records of endemic and cave-associated taxa within both limestone outcrop districts underscore the importance of allopatric speciation in shaping species composition in this region. This pattern is corroborated by studies on other taxa, such as spiny orb-web spiders (Magalhaes et al. 2024) and frogs (Teixeira et al. 2012).

5. Conclusion

The two newly described species of Pholcidae from semiarid Brazilian Caatinga environments do not fit into any of the previously available subfamilies. Genomic data suggest that together they are the sister taxon of a large clade of Pholcidae that includes several subfamilies. We conservatively join these two species in a single new genus Caipira in the new subfamily Caipirinae, even though there are some morphological differences between them that are uncommon within Pholcidae genera. Based of superficial similarities, our initial hypothesis was that the new Brazilian species might be related to the Chilean genus Aucana Huber, 2000. We thus also generated first molecular data for Aucana. These data reject our initial hypothesis and place Aucana in a clade that was previously informally called “other Arteminae” (Huber et al. 2018) and for which we propose the formal name Physocyclinae subfam. nov.; the revised subfamily-level relationships in Pholcidae are thus: (Pholcinae, Smeringopinae), (Caipirinae, ((Arteminae, Ninetinae), (Physocyclinae, Modisiminae))).

6. Declarations

Author contributions. GM: molecular methodology, curation and analysis of molecular data, writing; LSC: permits, collecting, biogeography, writing; LP: coordination of molecular methodology, analysis of molecular data; BAH: initiation of project, collecting, taxonomy, SEM, writing.

7. Acknowledgements

We thank Anja Bodenheim and Sandra Kukowka (LIB, Bonn) for their help with molecular lab work, Richard A. Torres Contreras and Alexandre S. Michelotto for help with field work in Brazil, and Abel Pérez-González and an anonymous referee for valuable comments on the manuscript. Specimens were collected under sampling permits issued by the Instituto Chico Mendes de Conservação da Biodiversidade through the Sistema de Autorização e Informação em Biodiversidade (SISBio; #59280-5). Field expeditions were supported by Fundação de Amparo à Pesquisa do Estado de Minas Gerais – FAPEMIG (PPM-00605-17 to Adalberto J. Santos), Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq (311843/2022-0 to LSC), Fundação de Amparo à Pesquisa do Estado do Piauí - FAPEPI (Termo de Aceitação e Outorga N° 001/2022 to LSC), and the German Research Foundation (DFG, project HU980/12-1 to BAH). The DFG is also acknowledged for funding molecular work and the PhD position of GM (project HU980/12-1). This publication is registered in compliance with Brazilian regulations at the Sistema Nacional de Gestão do Patrimônio Genético e do Conhecimento Tradicional Associado (SISGen; #A4CC17C).

8. References

Aharon S, Huber BA, Gavish-Regev E (2017) Daddy-long-leg giants: revision of the spider genus Artema Walckenaer, 1837 (Araneae, Pholcidae). European Journal of Taxonomy 376: 1–57. http://doi.org/10.5852/ejt.2017.376

Ázara LN, Hara MR, Ferreira RL (2020) Cladistic analysis of the Brazilian troglobitic harvestmen genus Iandumoema Pinto-da-Rocha (Opiliones: Gonyleptidae) with the description of three new species: a brief exercise over the use of troglomorphisms in cladistic analysis. Invertebrate Systematics 34: 474–503. https://doi.org/10.1071/IS19037

Bockmann FA, Castro R (2010) The blind catfish from the caves of Chapada Diamantina, Bahia, Brazil (Siluriformes: Heptapteridae): description, anatomy, phylogenetic relationships, natural history, and biogeography. Neotropical Ichthyology 8: 673–706. https://doi.org/10.1590/S1679-62252010000400001

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15): 2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Boni MF, Posada D, Feldman MW (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176(2): 1035–1047. https://doi.org/10.1534/genetics.106.068874

Brown BV (1993) A further chemical alternative to critical-point-drying for preparing small (or large) flies. Fly Times 11: 10.

Bueno AA de P, Bichuette ME, Zepon T, Penoni LR (2022) A new species of the troglobitic genus Spelaeogammarus da Silva Brum, 1975 (Amphipoda: Artesiidae) from a cave in the Brazilian semi-arid region, with new records of its congener, Spelaeogammarus spinilacertus Koenemann and Holsinger, 2000. Nauplius 30: 1–17. https://doi.org/10.1590/2358-2936e2022020

Capella-Gutiérrez SJ, Silla-Martínez M, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25(15): 1972–1973. https://doi.org/10.1093/bioinformatics/btp348

Cardoso GM, Bastos-Pereira R, Souza LA, Ferreira RL (2021) Chaimowiczia: a new Iuiuniscinae genus from Brazil (Oniscidea, Synocheta, Styloniscidae) with the description of two new troglobitic species. Subterranean Biology 39: 45–62. https://doi.org/10.3897/subtbiol.39.65305

Cardoso GM, Bastos-Pereira R, Ferreira RL (2022) Two new troglobitic species of Iansaoniscus from Brazilian caves (Crustacea, Isopoda, Pudeoniscidae). Subterranean Biology 43: 127–143. https://doi.org/10.3897/subtbiol.43.81308

Chifman J, Kubatko L (2014) Quartet inference from SNP data under the coalescent model. Bioinformatics 30(23): 3317–3324. https://doi.org/10.1093/bioinformatics/btu530

Dimitrov D, Astrin JJ, Huber BA (2013) Pholcid spider molecular systematics revisited, with new insights into the biogeography and the evolution of the group. Cladistics 29(2): 132–146. https://doi.org/10.1111/j.1096-0031.2012.00419.x

Duchêne DA, Mather N, Van Der Wal C, Ho SYW (2022) Excluding loci with substitution saturation improves inferences from phylogenomic data. Systematic Biology 71(3): 676–689. https://doi.org/10.1093/sysbio/syab075

Eberle J, Dimitrov D, Valdez-Mondragón A, Huber BA (2018) Microhabitat change drives diversification in pholcid spiders. BMC Evolutionary Biology 18: 141. https://doi.org/10.1186/s12862-018-1244-8

Esposito LA, Yamaguti HY, Souza CA, Pinto-Da-Rocha R, Prendini L (2017) Systematic revision of the Neotropical club-tailed scorpions, Physoctonus, Rhopalurus, and Troglorhopalurus, revalidation of Heteroctenus, and descriptions of two new genera and three new species (Buthidae: Rhopalurusinae). Bulletin of the American Museum of Natural History 415: 1–136. https://doi.org/10.1206/0003-0090-415.1.1

Faircloth BC (2016) PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32(5): 786–788. https://doi.org/10.1093/bioinformatics/btv646

Ferreira RL, Souza MFVR, Machado EO, Brescovit AD (2011) Description of a new Eukoenenia (Palpigradi: Eukoeneniidae) and Metagonia (Araneae: Pholcidae) from Brazilian caves, with notes on their ecological interactions. Journal of Arachnology 39: 409–419. https://doi.org/10.1636/Ha11-03.1

Ferreira RL, Berbert-Born M, Souza-Silva M (2023) The Água Clara cave system in northeastern Brazil: the richest hotspot of subterranean biodiversity in South America. Diversity 15: 761. https://doi.org/10.3390/d15060761

Ginestet C (2011) ggplot2: Elegant graphics for data analysis. Journal of the Royal Statistical Society Series A: Statistics in Society 174: 245–246. https://doi.org/10.1111/j.1467-985X.2010.00676_9.x

Gnaspini P, Vanin SA, Godoy NM (1997) A new genus of troglobitic carabid beetle from Brazil (Coleoptera, Carabidae, Zuphiini). Papéis Avulsos de Zoologia 40: 297–309. https://doi.org/10.11606/0031-1049.1997.40.p297-309

Huber BA (2000) New World pholcid spiders (Araneae: Pholcidae): a revision at generic level. Bulletin of the American Museum of Natural History 254: 1–348. https://doi.org/10.1206/0003-0090(2000)254<0001:NWPSAP>2.0.CO;2

Huber BA (2003) Southern African pholcid spiders: revision and cladistic analysis of Quamtana gen. nov. and Spermophora Hentz (Araneae: Pholcidae), with notes on male-female covariation. Zoological Journal of the Linnean Society 139: 477–527. https://doi.org/10.1046/j.0024-4082.2003.00082.x

Huber BA (2005) High species diversity, male-female coevolution, and metaphyly in Southeast Asian pholcid spiders: the case of Belisana Thorell 1898 (Araneae, Pholcidae). Zoologica 155: 1–126.

Huber BA (2011a) Revision and cladistic analysis of Pholcus and closely related taxa (Araneae, Pholcidae). Bonner Zoologische Monographien 58: 1–509.

Huber BA (2011b) Phylogeny and classification of Pholcidae (Araneae): an update. The Journal of Arachnology 39: 211–222. https://doi.org/10.1636/CA10-57.1

Huber BA (2012) Revision and cladistic analysis of the Afrotropical endemic genus Smeringopus Simon, 1890 (Araneae: Pholcidae). Zootaxa 3461: 1–138. https://doi.org/10.11646/zootaxa.3461.1.1

Huber BA (2013) Revision and cladistic analysis of the Guineo-Congolian spider genus Smeringopina Kraus (Araneae, Pholcidae). Zootaxa 3713: 1–160. https://doi.org/10.11646/zootaxa.3713.1.1

Huber BA (2018) The South American spider genera Mesabolivar and Carapoia (Araneae, Pholcidae): new species and a framework for redrawing generic limits. Zootaxa 4395: 1–178. https://doi.org/10.11646/zootaxa.4395.1.1

Huber BA (2019) The pholcid spiders of Sri Lanka (Araneae: Pholcidae). Zootaxa 4550: 1–57. https://doi.org/10.11646/zootaxa.4550.1.1

Huber BA (2021) Beyond size: sexual dimorphisms in pholcid spiders. Arachnology 18: 656–677. https://doi.org/10.13156/arac.2020.18.7.656

Huber BA (2022) Revisions of Holocnemus and Crossopriza: the spotted-leg clade of Smeringopinae (Araneae, Pholcidae). European Journal of Taxonomy 795: 1–241. https://doi.org/10.5852/ejt.2022.795.1663

Huber BA, Villarreal O (2020) On Venezuelan pholcid spiders (Araneae, Pholcidae). European Journal of Taxonomy 718: 1–317. https://doi.org/10.5852/ejt.2020.718.1101

Huber BA, Eberle J, Dimitrov D (2018) The phylogeny of pholcid spiders: a critical evaluation of relationships suggested by molecular data (Araneae, Pholcidae). ZooKeys 789: 51–101. https://doi.org/10.3897/zookeys.789.22781

Huber BA, Meng G, Acurio AE, Astrin JJ, Inclán DJ, Izquierdo M, Valdez-Mondragón A (2022) Metagonia spiders of Galápagos: blind cave-dwellers and their epigean relatives (Araneae, Pholcidae). Invertebrate Systematics 36: 647–678. https://doi.org/10.1071/IS21082

Huber BA, Meng G, Král J, Ávila Herrera IM, Izquierdo MA (2023a) Revision of the South American Ninetinae genus Guaranita (Araneae, Pholcidae). European Journal of Taxonomy 900: 32–80. https://doi.org/10.5852/ejt.2023.900.2301

Huber BA, Meng G, Král J, Ávila Herrera IM, Izquierdo MA, Carvalho LS (2023b) High and dry: integrative taxonomy of the Andean spider genus Nerudia (Araneae: Pholcidae). Zoological Journal of the Linnean Society 198: 534–591. https://doi.org/10.1093/zoolinnean/zlac100

Huber BA, Meng G, Král J, Ávila Herrera IM, Carvalho LS (2024a) Diamonds in the rough: Ibotyporanga (Araneae, Pholcidae) spiders in semi-arid Neotropical environments. European Journal of Taxonomy 963: 1–169. https://doi.org/10.5852/ejt.2024.963.2687

Huber BA, Meng G, Valdez-Mondragón A (2024b) Notes on Chisosa (Araneae: Pholcidae), with the description of a new species from Mexico. Zootaxa 5419: 217–244. https://doi.org/10.11646/zootaxa.5419.2.3

Jiang T, Kearney P, Li M (2001) A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM Journal on Computing 30(6): 1942–1961. https://doi.org/10.1137/S0097539799361683

Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14(6): 587–589. https://doi.org/10.1038/nmeth.4285

Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30(4): 772–780. https://doi.org/10.1093/molbev/mst010

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A (2019) RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35(21): 4453–4455. https://doi.org/10.1093/bioinformatics/btz305

Kulkarni S, Wood HM, Hormiga G (2023) Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies. Cladistics 39: 479–532. https://doi.org/10.1111/cla.12557

Lam HM, Ratmann O, Boni MF (2018) Improved algorithmic complexity for the 3SEQ recombination detection algorithm. Molecular Biology and Evolution 35(1): 247–251. https://doi.org/10.1093/molbev/msx263

Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Systematic Biology 62(4): 611–615. https://doi.org/10.1093/sysbio/syt022

Machado EO, Ferreira RL, Brescovit AD (2011) A new troglomorphic Metagonia Simon, 1893 (Araneae, Pholcidae) from Brazil. Zootaxa 3135(1): 59–62. https://doi.org/10.11646/zootaxa.3135.1.4

Magalhaes ILF, Martins PH, Faleiro BT, Vidigal THDA, Santos FR, Carvalho LS, Santos AJ (2024) Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands and landmasses, and indicates that Andean orogeny promotes speciation. Cladistics 40: 552–575. https://doi.org/10.1111/cla.12593

Meng G, Dimitrov D, Podsiadlowski L, Huber BA (2025) The complex interplay between evolutionary flexibility and diversification in a family of spiders. Systematic Biology, 2025: syaf070. https://doi.org/10.1093/sysbio/syaf070

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37(5): 1530–1534. https://doi.org/10.1093/molbev/msaa015

Monte BGO, Bichuette ME (2020) Taxonomic distinctness of the subterranean fauna from Peruaçu Caves National Park, state of Minas Gerais, eastern Brazil. Biota Neotropica 20: 1–20. https://doi.org/10.1590/1676-0611-bn-2019-0810

Moro MF, Amorim VO, de Queiroz LP, da Costa LRF, Maia RP, Taylor NP, Zappi DC (2024) Biogeographical districts of the Caatinga dominion: a proposal based on geomorphology and endemism. The Botanical Review 90: 376–429. https://doi.org/10.1007/s12229-024-09304-5

Naser-Khdour S, Minh BQ, Zhang W, Stone EA, Lanfear R (2019) The prevalence and impact of model violations in phylogenetic analysis. Genome Biology and Evolution 11(12): 3341–3352. https://doi.org/10.1093/gbe/evz193

Nichols JA, Pennington RT, Koenen EJM, Hughes CE, Hearn J, Bunnefeld L, Dexter KG, Stone GN, Kidner CA (2015) Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). Frontiers in Plant Science 6: 710. https://doi.org/10.3389/fpls.2015.00710

Pérez-González A, Ceccarelli FS, Monte BGO, Proud DN, DaSilva MB, Bichuette ME (2017) Light from dark: A relictual troglobite reveals a broader ancestral distribution for kimulid harvestmen (Opiliones: Laniatores: Kimulidae) in South America. PLOS ONE 12: e0187919. https://doi.org/10.1371/journal.pone.0187919

Polhemus DA, Ferreira RL (2018) Two unusual new genera of cavernicolous Hydrometridae (Insecta: Heteroptera) from eastern Brazil. Tijdschrift voor Entomologie 161: 25–38. https://doi.org/10.1163/22119434-00002072

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A (2020) Using SPAdes de novo assembler. Current Protocols in Bioinformatics 70(1): e102. https://doi.org/10.1002/cpbi.102

R Core Team (2020) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.

Sayyari E, Whitfield JB, Mirarab S (2018) DiscoVista: Interpretable visualizations of gene tree discordance. Molecular Phylogenetics and Evolution 122: 110–115. https://doi.org/10.1016/j.ympev.2018.01.019

Seemann T (2017) Shovill: Faster SPAdes assembly of Illumina reads. https://github.com/tseemann/shovill

Simon E (1893) Histoire Naturelle des Araignées. 2^nd edition, 1(2): 256–488. Roret, Paris.

Strimmer K, von Haeseler A (1997) Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proceedings of the National Academy of Sciences U.S.A. 94(13): 6815–6819. https://doi.org/10.1073/pnas.94.13.6815

Swofford DL (2002) PAUP: phylogenetic analysis using parsimony (and other methods), 4.0 beta. http://paup.csit.fsu.edu

Teixeira M, Amaro RC, Recoder RS, De Sena MA, Rodrigues MT (2012) A relict new species of Oreobates (Anura, Strabomantidae) from the Seasonally Dry Tropical Forests of Minas Gerais, Brazil, and its implication to the biogeography of the genus and that of South American Dry Forests. Zootaxa 3158: 37–52. https://doi.org/10.11646/zootaxa.3158.1.3

Vachaspati P, Warnow T (2018) SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space. Molecular Phylogenetics and Evolution 124: 122–136. https://doi.org/10.1016/j.ympev.2018.03.006

Zhang C, Mirarab S (2022) Weighting by gene tree uncertainty improves accuracy of quartet-based species trees. Molecular Biology and Evolution 39(12): msac215. https://doi.org/10.1093/molbev/msac215

Supplementary materials

Supplementary material 1

Figures S1–S4

Meng G, Carvalho LS, Podsiadlowski L, Huber BA (2026)

Data type: .zip

Explanation notes: Figure S1. Missing data distribution of matrix 1. The missing proportion of a contig of a locus was obtained by dividing the number of dashes (dashes and Ns) of the contig by the locus length. Visualization was performed with ggplot2. — Figure S2. Statistics of data matrix 1. Density distributions of characteristics including average GC content, GC content interquartile range, number and proportion of missing data (dashes and Ns), number and proportion of parsimony-informative sites, length of the multiple sequence alignment (MSA), and number of taxa in the MSA. Visualizations were performed with ggplot2. — Figure S3. Likelihood mapping analysis of matrix 1. The IQ-TREE was used for the analysis. — Figure S4. Known geographic distribution of Caipira gen. nov., including spider sampling localities in the region.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.

Download file (1.53 MB)

Supplementary material 2

Tables S1–S6

Meng G, Carvalho LS, Podsiadlowski L, Huber BA (2026)

Data type: .zip

Explanation notes: Table S1. Sample information for UCE-based phylogenetic analysis. — Table S2. Data matrix (1–5) statistics. — Table S3. Tests of symmetry of matrix 1. The IQ-TREE was used for the analysis. — Table S4. PhyloMAd was used to assess substitutional saturation based on matrix 1. — Table S5. Intralocus recombination analysis with 3SEQ based on matrix 1. — Table S6. Species excluded from the comparative analysis of leg proportions.

Download file (622.73 kb)