Submit to Diversity Review for Diversity Propose a Special Issue

Journal Menu

Journal Browser

► Journal Browser

Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (1 October 2021) | Viewed by 50921

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology book cover image

Share This Special Issue

Special Issue Editor

Dr. Matjaž Kuntner

E-Mail Website
Guest Editor

Department of Organisms and Ecosystems Research, National Institute of Biology, 1000 Ljubljana, Slovenia
Interests: phylogenetic systematics; phenotypic evolution; spiders; biogeography; genomics; silk

Special Issue Information

Dear Colleagues,

I would like to invite you to contribute to an upcoming Special Issue of Diversity, titled “Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology”.

Arachnids represent a hyperdiverse, yet understudied, group of invertebrate animals. The diversity of spiders, scorpions, and harvestmen may be relatively well documented, while additional orders remain enigmatic. Only a handful of arachnid genomes have so far been annotated, but genomic data are beginning to be utilized in phylogenetic analyses at species and higher taxonomic levels. In fact, systematics focusing on arachnids has been at the forefront of this discipline, with recent contributions uncovering the utility of transcriptomic and genomic data in deciphering the tree of life. Into this wealth of phylogenomic data, arachnologists routinely weave phenotypic and ecological variables for truly integrative evolutionary studies. Arachnids show diverse, and oftentimes clade-predictable, patterns in dispersal biology. As a consequence, some clades have become textbook examples of vicariant biogeography, while others, e.g., those traveling aerially by silken sails, maintain lively patterns of gene flow over continents. Together, arachnids can help us understand the Earth’s biogeographic history as well as the evolution of complex biodiversity hotspots. Arachnids range from sub-millimeter to dinner plate sizes, and exhibit an astonishing array of morphologies and sexual biologies, making them excellent models in the study of the interplay of natural and sexual selection. Considering arachnid age and deep phylogenetic splits, their evolutionary landscape is uniquely diverse, and calls for new original and synthetic research.

This volume aims to contribute to advancing or reviewing phylogenomic, biogeographic, and evolutionary research trends in arachnid research. We welcome your original research papers, perspectives, and reviews with a focus on any arachnid order, on any evolutionary topic, from any region of the globe. Taxonomic papers are welcome, as long as they advance our understanding of arachnid evolution, biogeography, or phylogenetic systematics.

I am looking forward to your submissions.

Dr. Matjaž Kuntner
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

tree of life
Arachnida
genomics
biological diversity
biogeographic history
integrative taxonomy
evolutionary analyses

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (13 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Editorial

Jump to: Research, Review

5 pages, 195 KiB

Open AccessEditorial

Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology

by Matjaž Kuntner

Diversity 2022, 14(5), 347; https://doi.org/10.3390/d14050347 - 28 Apr 2022

Cited by 1 | Viewed by 2096

Abstract

Textbook knowledge tells us that arachnids are a hyper diverse clade of chelicerates that have taken on terrestrial lifestyles [...] Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

Research

Jump to: Editorial, Review

28 pages, 70752 KiB

Open AccessEditor’s ChoiceArticle

Island–to–Island Vicariance, Founder–Events and within–Area Speciation: The Biogeographic History of the Antillattus Clade (Salticidae: Euophryini)

by Franklyn Cala-Riquelme, Patrick Wiencek, Eduardo Florez-Daza, Greta J. Binford and Ingi Agnarsson

Diversity 2022, 14(3), 224; https://doi.org/10.3390/d14030224 - 18 Mar 2022

Cited by 7 | Viewed by 4118

Abstract

The Caribbean Archipelago is a biodiversity hotspot that plays a key role in developing our understanding of how dispersal ability affects species formation. In island systems, species with intermediate dispersal abilities tend to exhibit greater diversity, as may be the case for many of the salticid lineages of the insular Caribbean. Here, we use molecular phylogenetic analyses to infer patterns of relationships and biogeographic history of the Caribbean endemic Antillattus clade (Antillattus, Truncattus, and Petemethis). We test if the timing of origin of the Antillatus clade in the Greater Antilles is congruent with GAARlandia and infer patterns of diversification within the Antillattus clade among Cuba, Hispaniola, and Puerto Rico. Specifically, we evaluate the relative roles of dispersal over land connections, and overwater dispersal events in diversification within the Greater Antilles. Time tree analysis and model-based inference of ancestral ranges estimated the ancestor of the Antillattus clade to be c. 25 Mya, and the best model suggests dispersal via GAARlandia from northern South America to Hispaniola. Hispaniola seems to be the nucleus from which ancestral populations dispersed into Cuba and Puerto Rico via land connections prior to the opening of the Mona Passage and the Windward Passage. Divergences between taxa of the Antillattus clade from Cuban, Hispaniolan, and Puerto Rican populations appear to have originated by vicariance, founder-events and within-island speciation, while multiple dispersal events (founder-events) between Cuba and Hispaniola during the Middle Miocene and the Late Miocene best explain diversity patterns in the genera Antillattus and Truncattus. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

14 pages, 2979 KiB

Open AccessArticle

In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae)

by Yi-Yen Li, Jer-Min Tsai, Cheng-Yu Wu, Yi-Fan Chiu, Han-Yun Li, Natapot Warrit, Yu-Cen Wan, Yen-Po Lin, Ren-Chung Cheng and Yong-Chao Su

Diversity 2022, 14(3), 184; https://doi.org/10.3390/d14030184 - 3 Mar 2022

Cited by 3 | Viewed by 2664

Abstract

Reduced-representation sequencing (RRS) has made it possible to identify hundreds to thousands of genetic markers for phylogenomic analysis for the testing of phylogenetic hypotheses in non-model taxa. The use of customized probes to capture genetic markers (i.e., ultraconserved element (UCE) approach) has further boosted the efficiency of collecting genetic markers. Three UCE probe sets pertaining to spiders (Araneae) have been published, including one for the suborder Mesothelae (an early diverged spider group), one for Araneae, and one for Arachnida. In the current study, we developed a probe set specifically for the superfamily Araneoidea in spiders. We then combined the three probe sets for Araneoidea, Araneae, and Arachnid into a fourth probe set. In testing the effectiveness of the 4 probe sets, we used the captured loci of the 15 spider genomes in silico (6 from Araneoidea). The combined probe set outperformed all other probe sets in terms of the number of captured loci. The Araneoidea probe set outperformed the Araneae and Arachnid probe sets in most of the included Araneoidea species. The reconstruction of phylogenomic trees using the loci captured from the four probe sets and the data matrices generated from 50% and 75% occupancies indicated that the node linked to the Stegodyphus + RTA (retrolateral tibial apophysis) clade has unstable nodal supports in the bootstrap values, gCFs, and sCFs. Our results strongly indicate that developing ad hoc probe sets for sub-lineages is important in the cases where the origins of a lineage are ancient (e.g., spiders ~380 MYA). Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

13 pages, 1523 KiB

Open AccessArticle

New Distributional Records of Phidippus (Araneae: Salticidae) for Baja California and Mexico: An Integrative Approach

by Luis C. Hernández Salgado, Dariana R. Guerrero Fuentes, Luz A. Garduño Villaseñor, Lita Castañeda Betancur, Eulogio López Reyes and Fadia Sara Ceccarelli

Diversity 2022, 14(3), 159; https://doi.org/10.3390/d14030159 - 24 Feb 2022

Cited by 3 | Viewed by 3013

Abstract

Because of its heterogeneity in ecoregions and its varied topography, the Mexican peninsula of Baja California (BCP) is an area of high diversity for many taxa, including spiders. However, a paucity of studies means that the diversity of BCP’s spiders is generally poorly known. The North American jumping spider genus Phidippus comprises over 60 species, of which approximately 45% are found in Mexico. Among those, 6 have been recorded to date from the BCP but adding up the species recorded in nearby states, up to 20 more can be expected. As part of a larger study on the evolution and biogeography of the North American genus Phidippus, the aim here was to explore the diversity of the genus in the BCP using an integrative taxonomic approach and to present new distributional records. Until now, at least ten species have been collected from the BCP, one of which is a new record for Mexico, three new records for the BCP, and at least one undescribed species. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

26 pages, 3641 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Single-Island Endemism despite Repeated Dispersal in Caribbean Micrathena (Araneae: Araneidae): An Updated Phylogeographic Analysis

by Lily Shapiro, Greta J. Binford and Ingi Agnarsson

Diversity 2022, 14(2), 128; https://doi.org/10.3390/d14020128 - 10 Feb 2022

Cited by 8 | Viewed by 4032

Abstract

Island biogeographers have long sought to elucidate the mechanisms behind biodiversity genesis. The Caribbean presents a unique stage on which to analyze the diversification process, due to the geologic diversity among the islands and the rich biotic diversity with high levels of island endemism. The colonization of such islands may reflect geologic heterogeneity through vicariant processes and/ or involve long-distance overwater dispersal. Here, we explore the phylogeography of the Caribbean and proximal mainland spiny orbweavers (Micrathena, Araneae), an American spider lineage that is the most diverse in the tropics and is found throughout the Caribbean. We specifically test whether the vicariant colonization via the contested GAARlandia landbridge (putatively emergent 33–35 mya), long-distance dispersal (LDD), or both processes best explain the modern Micrathena distribution. We reconstruct the phylogeny and test biogeographic hypotheses using a ‘target gene approach’ with three molecular markers (CO1, ITS-2, and 16S rRNA). Phylogenetic analyses support the monophyly of the genus but reject the monophyly of Caribbean Micrathena. Biogeographical analyses support five independent colonizations of the region via multiple overwater dispersal events, primarily from North/Central America, although the genus is South American in origin. There is no evidence for dispersal to the Greater Antilles during the timespan of GAARlandia. Our phylogeny implies greater species richness in the Caribbean than previously known, with two putative species of M. forcipata that are each single-island endemics, as well as deep divergences between the Mexican and Floridian M. sagittata. Micrathena is an unusual lineage among arachnids, having colonized the Caribbean multiple times via overwater dispersal after the submergence of GAARlandia. On the other hand, single-island endemism and undiscovered diversity are nearly universal among all but the most dispersal-prone arachnid groups in the Caribbean. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

16 pages, 2047 KiB

Open AccessArticle

Solenysa, a Cretaceous Relict Spider Group in East Asia

by Jiahui Tian, Yongjia Zhan, Chengmin Shi, Hirotsugu Ono and Lihong Tu

Diversity 2022, 14(2), 120; https://doi.org/10.3390/d14020120 - 8 Feb 2022

Cited by 2 | Viewed by 2201

Abstract

A time scale of phylogenetic relationships contributes to a better understanding of the evolutionary history of organisms. Herein, we investigate the temporal divergence pattern that gave rise to the poor species diversity of the spider genus Solenysa in contrast with the other six major clades within linyphiids. We reconstructed a dated phylogeny of linyphiids based on multi-locus sequence data. We found that Solenysa diverged from other linyphiids early in the Cretaceous (79.29 mya), while its further diversification has been delayed until the middle Oligocene (28.62 mya). Its diversification trend is different from all of the other major lineages of linyphiids but is closely related with the Cenozoic ecosystem transition caused by global climate changes. Our results suggest that Solenysa is a Cretaceous relict group, which survived the mass extinction around the K-T boundary. Its low species diversity, extremely asymmetric with its sister group, is largely an evolutionary legacy of such a relict history, a long-time lag in its early evolutionary history that delayed its diversification. The limited distribution of Solenysa species might be related to their extreme dependence on highly humid environments. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

15 pages, 436 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Improving Taxonomic Practices and Enhancing Its Extensibility—An Example from Araneology

by Jason E. Bond, Rebecca L. Godwin, Jordan D. Colby, Lacie G. Newton, Xavier J. Zahnle, Ingi Agnarsson, Chris A. Hamilton and Matjaž Kuntner

Diversity 2022, 14(1), 5; https://doi.org/10.3390/d14010005 - 23 Dec 2021

Cited by 19 | Viewed by 5890

Abstract

Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely available, whether an explicit species hypothesis was stated, what types of media were used, the sample sizes, and the degree to which species constructs were integrative. The findings we report reveal that taxonomy remains largely descriptive, not integrative, and provides no explicit conceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-third of all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies made data freely available, and only ~14% of all newly described species employed more than one line of evidence, with molecular data used in ~6% of the studies. These same trends have been discovered in other animal groups, and therefore we find it logical that taxonomists face an uphill challenge when justifying the scientific rigor of their field and securing the needed resources. To move taxonomy forward, we make recommendations that, if implemented, will enhance its rigor, repeatability, and scientific standards. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

18 pages, 2968 KiB

Open AccessEditor’s ChoiceArticle

Biogeography of Long-Jawed Spiders Reveals Multiple Colonization of the Caribbean

by Klemen Čandek, Ingi Agnarsson, Greta J. Binford and Matjaž Kuntner

Diversity 2021, 13(12), 622; https://doi.org/10.3390/d13120622 - 26 Nov 2021

Cited by 7 | Viewed by 3127

Abstract

Dispersal ability can affect levels of gene flow thereby shaping species distributions and richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. Here, we tested this prediction on long-jawed spiders (Tetragnatha) of the Caribbean archipelago using phylogenies from a total of 318 individuals delineated into 54 putative species. Our results support a Tetragnatha monophyly (within our sampling) but reject the monophyly of the Caribbean lineages, where we found low endemism yet high diversity. The reconstructed biogeographic history detects a potential early overwater colonization of the Caribbean, refuting an ancient vicariant origin of the Caribbean Tetragnatha as well as the GAARlandia land-bridge scenario. Instead, the results imply multiple colonization events to and from the Caribbean from the mid-Eocene to late-Miocene. Among arachnids, Tetragnatha uniquely comprises both excellently and poorly dispersing species. A direct test of the IDM would require consideration of three categories of dispersers; however, long-jawed spiders do not fit one of these three a priori definitions, but rather represent a more complex combination of attributes. A taxon such as Tetragnatha, one that readily undergoes evolutionary changes in dispersal propensity, can be referred to as a ‘dynamic disperser’. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

17 pages, 13574 KiB

Open AccessArticle

Beta Diversity along an Elevational Gradient at the Pico da Neblina (Brazil): Is Spider (Arachnida-Araneae) Community Composition Congruent with the Guayana Region Elevational Zonation?

by André A. Nogueira, Antonio D. Brescovit, Gilmar Perbiche-Neves and Eduardo M. Venticinque

Diversity 2021, 13(12), 620; https://doi.org/10.3390/d13120620 - 26 Nov 2021

Cited by 3 | Viewed by 2832

Abstract

Beta diversity is usually high along elevational gradients. We studied a spider community at the Pico da Neblina (Brazil), an Amazonian mountain which is one of the southern components of the Guayana region. We sampled six elevations and investigated if beta diversity patterns correspond to the elevational division proposed for the region, between lowlands (up to 500 m), uplands (500 m to 1500 m), and highlands (>1500 m). Patterns of dominance increased with elevation along the gradient, especially at the two highest elevations, indicating that changes in composition may be accompanied by changes in species abundance distribution. Beta diversity recorded was very high, but the pattern observed was not in accordance with the elevationaldivision proposed for the region. While the highlands indeed harbored different fauna, the three lowest elevationshad similar species compositions, indicating that the lowlands spider community extends into the uplands zone. Other measures of compositional change, such as similarity indices and species indicator analysis, also support this pattern. Our results, in addition to a revision of the literature, confirm the high diversity and endemism rates of montane spider communities, and we stress the importance of protecting those environments, especially considering the climate crisis. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

16 pages, 3804 KiB

Open AccessArticle

Old Brains in Alcohol: The Usability of Legacy Collection Material to Study the Spider Neuroarchitecture

by F. Andres Rivera-Quiroz and Jeremy Abraham Miller

Diversity 2021, 13(11), 601; https://doi.org/10.3390/d13110601 - 21 Nov 2021

Cited by 2 | Viewed by 2600

Abstract

Natural history collections include rare and significant taxa that might otherwise be unavailable for comparative studies. However, curators must balance the needs of current and long-term research. Methods of data extraction that minimize the impact on specimens are therefore favored. Micro-CT has the potential to expose new character systems based on internal anatomy to taxonomic and phylogenetic analysis without dissection or thin sectioning for histology. However, commonly applied micro-CT protocols involve critical point drying, which permanently changes the specimen. Here, we apply a minimally destructive method of specimen preparation for micro-CT investigation of spider neuroanatomy suitable for application to legacy specimens in natural history collections. We used two groups of female spiders of the common species Araneus diadematus—freshly captured (n = 11) vs. legacy material between 70 and 90 years old (n = 10)—to qualitatively and quantitatively assess the viability of micro-CT scanning and the impact of aging on their neuroarchitecture. We statistically compared the volumes of the supraesophageal ganglion (syncerebrum) and used 2D geometric morphometrics to analyze variations in the gross shape of the brain. We found no significant differences in the brain shape or the brain volume relative to the cephalothorax size. Nonetheless, a significant difference was observed in the spider size. We considered such differences to be explained by environmental factors rather than preservation artifacts. Comparison between legacy and freshly collected specimens indicates that museum specimens do not degrade over time in a way that might bias the study results, as long as the basic preservation conditions are consistently maintained, and where lapses in preservation have occurred, these can be identified. This, together with the relatively low-impact nature of the micro-CT protocol applied here, could facilitate the use of old, rare, and valuable material from collections in studies of internal morphology. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

14 pages, 3179 KiB

Open AccessArticle

A Natural Colonisation of Asia: Phylogenomic and Biogeographic History of Coin Spiders (Araneae: Nephilidae: Herennia)

by Eva Turk, Jason E. Bond, Ren-Chung Cheng, Klemen Čandek, Chris A. Hamilton, Matjaž Gregorič, Simona Kralj-Fišer and Matjaž Kuntner

Diversity 2021, 13(11), 515; https://doi.org/10.3390/d13110515 - 22 Oct 2021

Cited by 5 | Viewed by 2887

Abstract

Reconstructing biogeographic history is challenging when dispersal biology of studied species is poorly understood, and they have undergone a complex geological past. Here, we reconstruct the origin and subsequent dispersal of coin spiders (Nephilidae: Herennia Thorell), a clade of 14 species inhabiting tropical Asia and Australasia. Specifically, we test whether the all-Asian range of Herennia multipuncta is natural vs. anthropogenic. We combine Anchored Hybrid Enrichment phylogenomic and classical marker phylogenetic data to infer species and population phylogenies. Our biogeographical analyses follow two alternative dispersal models: ballooning vs. walking. Following these assumptions and considering measured distances between geographical areas through temporal intervals, these models infer ancestral areas based on varying dispersal probabilities through geological time. We recover a wide ancestral range of Herennia including Australia, mainland SE Asia and the Philippines. Both models agree that H. multipuncta internal splits are generally too old to be influenced by humans, thereby implying its natural colonisation of Asia, but suggest quite different colonisation routes of H. multipuncta populations. The results of the ballooning model are more parsimonious as they invoke fewer chance dispersals over large distances. We speculate that coin spiders’ ancestor may have lost the ability to balloon, but that H. multipuncta regained it, thereby colonising and maintaining larger areas. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Figure 1

23 pages, 7979 KiB

Open AccessFeature PaperArticle

Incorporating Topological and Age Uncertainty into Event-Based Biogeography of Sand Spiders Supports Paleo-Islands in Galapagos and Ancient Connections among Neotropical Dry Forests

by Ivan L. F. Magalhaes, Adalberto J. Santos and Martín J. Ramírez

Diversity 2021, 13(9), 418; https://doi.org/10.3390/d13090418 - 31 Aug 2021

Cited by 19 | Viewed by 4014

Abstract

Event-based biogeographic methods, such as dispersal-extinction-cladogenesis, have become increasingly popular for attempting to reconstruct the biogeographic history of organisms. Such methods employ distributional data of sampled species and a dated phylogenetic tree to estimate ancestral distribution ranges. Because the input tree is often a single consensus tree, uncertainty in topology and age estimates are rarely accounted for, even when they may affect the outcome of biogeographic estimates. Even when such uncertainties are taken into account for estimates of ancestral ranges, they are usually ignored when researchers compare competing biogeographic hypotheses. We explore the effect of incorporating this uncertainty in a biogeographic analysis of the 21 species of sand spiders (Sicariidae: Sicarius) from Neotropical xeric biomes, based on a total-evidence phylogeny including a complete sampling of the genus. Using a custom R script, we account for uncertainty in ages and topology by estimating ancestral ranges over a sample of trees from the posterior distribution of a Bayesian analysis, and for uncertainty in biogeographic estimates by using stochastic maps. This approach allows for counting biogeographic events such as dispersal among areas, counting lineages through time per area, and testing biogeographic hypotheses, while not overestimating the confidence in a single topology. Including uncertainty in ages indicates that Sicarius dispersed to the Galapagos Islands when the archipelago was formed by paleo-islands that are now submerged; model comparison strongly favors a scenario where dispersal took place before the current islands emerged. We also investigated past connections among currently disjunct Neotropical dry forests; failing to account for topological uncertainty underestimates possible connections among the Caatinga and Andean dry forests in favor of connections among Caatinga and Caribbean + Mesoamerican dry forests. Additionally, we find that biogeographic models including a founder-event speciation parameter (“+J”) are more prone to suffer from the overconfidence effects of estimating ancestral ranges using a single topology. This effect is alleviated by incorporating topological and age uncertainty while estimating stochastic maps, increasing the similarity in the inference of biogeographic events between models with or without a founder-event speciation parameter. We argue that incorporating phylogenetic uncertainty in biogeographic hypothesis-testing is valuable and should be a commonplace approach in the presence of rogue taxa or wide confidence intervals in age estimates, and especially when using models including founder-event speciation. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Graphical abstract

Review

Jump to: Editorial, Research

33 pages, 5076 KiB

Open AccessFeature PaperEditor’s ChoiceReview

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

by Prashant P. Sharma, Jesús A. Ballesteros and Carlos E. Santibáñez-López

Diversity 2021, 13(11), 568; https://doi.org/10.3390/d13110568 - 6 Nov 2021

Cited by 19 | Viewed by 8135

Abstract

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

► Show Figures

Journal Menu

Journal Browser

Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (13 papers)

Editorial

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI