Matthew Van Dam

California Academy of Sciences · Department of Entomology

Graphical abstract Highlights d Coevolutionary interactions arise from community assembly events, not host tracking d Structural colors in model and mimetic systems use different nano-level mechanisms d We resolved the phylogeny of Doliops using a design of more than 30,000 UCE loci

We use integrative taxonomy to elucidate species boundaries of the plant bug genus Pseudoloxops (Kirkaldy 1905) in the Austral and Society archipelagos of French Polynesia. We operationalize the unified species concept by treating each individual as a potential species and then establish initial groupings (putative species) following statistically...

Pseudapocyrtus schadenbergi Heller, 1912 is reported for the first time since its description in Barangay Tanglagan in the lowland forests of the Apayao Lowland Forest Key Biodiversity Area. Characters for recognition are mentioned, high-definition photographs of its habitus, median lobe, and endophallus are provided, and a brief discussion of its...

Incredibly powerful whole genome studies of conservation genetics, evolution, and biogeography become possible for non-model organisms when reference genomes are available. Here, we report the sequence and assembly of the whole genome of the little vermilion flycatcher (Pyrocephalus nanus; Family Tyrannidae), which is an endemic, endangered, and de...

The fulgorid name Alphina glauca (Metcalf) has been used erroneously since its inception to refer to a primarily southeastern U.S. species described originally as Calyptoproctus marmoratus Spinola. Additionally, at least three undescribed species from the Southwest have been incorrectly identified as A. glauca. The holotype of A. glauca has not bee...

Tetraopes longhorn beetles are known for their resistance to milkweed plant toxins and their coevolutionary dynamics with milkweed plants (Asclepias). This association is considered a textbook example of coevolution, in which each species of Tetraopes is specialized to feed on one or a few species of Asclepias. A major challenge to investigating co...

We describe and illustrate two new species of Glenea Newman, 1842 from the Philippines: G. barsevskisi sp. nov. and G. vitali sp. nov. Both species belong to the subgenus Glenea sçnsű strictô. At present, the total number of Glenea species in the Philippines is 89 (79 species and 10 subspecies).

The evolutionary origins of mimicry in the Easter Egg weevil, Pachyrhynchus, have fascinated researchers since first noted more than a century ago by Alfred Russel Wallace. Müllerian mimicry, or mimicry in which two or more distasteful species look similar, is widespread throughout the animal kingdom. Given the varied but discrete color patterns in...

The evolutionary origins of mimicry in the Easter Egg weevil, Pachyrhynchus, have fascinated researchers since first noted more than a century ago by Alfred Russel Wallace. Müllerian mimicry, or mimicry in which two or more distasteful species look similar, is widespread throughout the animal kingdom. Given the varied but discrete color patterns in...

We use molecular phylogenomic as well as morphological data to provide a taxonomic update on New Guinea endemic Philaccolilus diving beetles. In these lotic beetles, we find cryptic diversity that highlights the need for geographically denser sampling combined with the use of an intergrative taxonomic approach to unravel the true diversity and biog...

The brilliant appearance of Easter Egg weevils, genus Pachyrhynchus (Coleoptera, Curculionidae), originates from complex dielectric nanostructures within their elytral scales and elytra. Previous work, investigating singular members of the Pachyrhynchus showed the presence of either quasi‐ordered or ordered 3D photonic crystals based on the single...

Phylogenomics via ultraconserved elements (UCEs) has led to improved phylogenetic reconstructions across the tree of life. However, inadvertently incorporating non‐targeted DNA into the UCE marker design will lead to misinformation being incorporated into subsequent analyses. To date, the effectiveness of basic metagenomic filtering strategies has...

Pachyrhynchus obumanuvu sp. nov., a new easter egg weevil discovered from the remaining forest patches in Davao region in Mindanao Island, Philippines is described, and a brief note of its ecology is also presented.

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source in...

The evolutionary origins of mimicry in the Easter Egg weevil, Pachyrhynchus , have fascinated researchers since first noted more than a century ago by Alfred Russel Wallace. Müllerian mimicry, or mimicry in which two or more distasteful species look similar, is widespread throughout the animal kingdom. Given the varied but discrete color patterns i...

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders? We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source in...

Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 11 phylog...

Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 11 phylog...

Despite the dominance of terrestriality in spiders, species across a diverse array of families are associated with aquatic habitats. Many species in the spider family Dictynidae are associated with water, either living near it or, in the case of Argyroneta aquatica, in it. Previous studies have indicated that this association arose once within the...

Despite the dominance of terrestriality in spiders, species across a diverse array of families are associated with aquatic habitats. Many species in the spider family Dictynidae are associated with water, either living near it or, in the case of Argyroneta aquatica, in it. Previous studies have indicated that this association arose once within the...

Ultraconserved genomic elements (UCEs), are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes is agnostic to genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 12 phylogenomic studies acros...

Aim Phenology, the temporal response of a population to its climate, is a crucial behavioral trait shared across life on earth. How species adapt their phenologies to climate change is poorly understood but critical in understanding how species will respond to future change. We use a group of flies ( Rhaphiomidas ) endemic to the North American de...

Aim Phenology, the temporal response of a population to its climate, is a crucial behavioral trait shared across life on earth. How species adapt their phenologies to climate change is poorly understood but critical in understanding how species will respond to future change. We use a group of flies (Rhaphiomidas) endemic to the North American deser...

Mites (Acari) are one of the most diverse groups of life on Earth, yet their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved g...

[This corrects the article DOI: 10.1371/journal.pone.0188044.].

Recent theoretical advances have hypothesized a central role of habitat persistence on population genetic structure and resulting biodiversity patterns of freshwater organisms. Here, we address the hypothesis that lotic species, or lineages adapted to comparably geologically stable running water habitats (streams and their marginal habitats), have...

The Habitat Template Concept applied to a freshwater system indicates that lotic species, or those which occupy permanent habitats along stream courses, are less dispersive than lentic species, or those that occur in more ephemeral aquatic habitats. Thus, populations of lotic species will be more structured than those of lentic species. Stream cour...

The 2016 International Weevil Meeting was held immediately after the International Congress of Entomology (ICE). It built on the topics and content of the 2016 ICE weevil symposium Phylogeny and Evolution of Weevils (Coleoptera: Curculionoidea): A Symposium in Honor of Dr. Guillermo "Willy" Kuschel. Beyond catalyzing research and collaboration, the...

Weevils (Curculionoidea) comprise one of the most diverse groups of organisms on earth. There is hardly a vascular plant or plant part without its own species of weevil feeding on it and weevil species diversity is greater than the number of fishes, birds, reptiles, amphibians and mammals combined. Here, we employ ultraconserved elements (UCEs) des...

Table of specimens used in this stud with museum where they are deposited the year the specimen was dispatched and the subsequent preservation type. Museum abbreviations as follows: SNSB-Zoological State Collection, München (ZSM), State Museum of Natural History Karlsruhe (SMNK), California Academy of Sciences (CAS). (XLS)

ASTRAL-RAxML partitioned Eupholini species tree, minus 10% lowest quantile of average bootstrap values and potentially oversaturated loci. (PDF)

Partitioning strategy by loci. (ZIP)

Results of UCE loci alignments percent completeness (number of taxa missing from total number of taxa). Matrix % complete indicate the percent completeness of the UCE loci alignments. 1st round of sequencing indicates the number of UCE loci alignments from the first round of sequencing of the 48 samples on an illumina HiSeq 3000 half lane. 2nd roun...

ASTRAL-RAxML partitioned Eupholini tree, minus 10% lowest quantile of average bootstrap values loci. (PDF)

Links to supporting R/unix code, alignments and raw sequence reads. (DOCX)

The underlying mechanisms responsible for the general increase in species richness from temperate regions to the tropics remain equivocal. Many hypotheses have been proposed to explain this astonishing pattern but additional empirical studies are needed to shed light on the drivers at work. Here we reconstruct the evolutionary history of the cosmop...

The hyperdiverse genus Trigonopterus has its center of diversity in Melanesia, but only a single species is recorded from the Bismarck Archipelago to date. Here we describe four new species from the island of New Britain: Trigonopterus chewbacca sp. n., Trigonopterus obsidianus sp. n., Trigonopterus puncticollis sp. n. and Trigonopterus silaliensis...

Aim To examine the role of geological history, connectivity and distance in shaping the biogeographical structure of North American desert clades that are restricted to habitat islands (sand dunes and relictual aquatic habitats), using statistical model choice on old and new probabilistic biogeographical models. Location North America, Mojave, Son...

The Sunda Arc forms an almost continuous chain of islands and thus a potential dispersal corridor between mainland Southeast Asia and Melanesia. However, the Sunda Islands have rather different geological histories, which might have had an important impact on actual dispersal routes and community assembly. Here, we reveal the biogeographical histor...

The genus Miloderes Casey, 1888 is reviewed and three new species are described. The genus now has eight valid species: M. amargosensis sp. nov., M. mercuryensis Tanner, M. nelsoni Kissinger, M. panamintensis sp. nov., M. setosus Casey, M. tingi Tanner, M. ubehebensis sp. nov. and M. viridis Pierce. Miloderes allredi Tanner, 1974 is a new junior sy...

A simple, rapid technique is presented for the eversion of the endophallus in the Curculionoidea. The endophallus is inflated using the introduction of a viscous gel from a syringe inserted in the base of the median lobe, which is held in place by Pierse corneal forceps. This relatively time-efficient technique works on a wide size range and taxono...

Island systems have been indispensablein understanding the processes generating biodiversity. Examples from the Galapagos, Caribbeanand Hawaiian archipelagos demonstrate the utility of islands for the study ofadaptation, community assembly, and speciation. In addition to oceanic islands,habitat islands are also of great interest to evolutionary bio...

This paper describes one new species, Rhaphiomidas ballmeri sp. nov. from Sonora state, Mexico. A new key is provided for males of this genus to aid in their identification.

Larvae of the genus Pseudocotalpa Hardy, 1971 are described for the first time based on the larva of P. sonorica Hardy 1974. Characters used to separate Pseudocotalpa from similar genera are given. Life history observations of adults of P. sonorica are also given.

The sand dunes of the Southwest deserts of the United States and Mexico hold a unique assemblage of plants and animals. The island-like nature of sand dunes, and the extreme conditions they present, requires that many species be uniquely adapted for life in these environments. More detailed studies of the biogeographic and ecological characteristic...

Scarab diversity in the Algodones Dunes (Imperial Co., CA) was assessed using a series of light-bucket transects to ascertain the impact of off-road vehicle (ORV) use. We compared dune endemic scarab species on the dunes south of Hwy. 78 that receive intense ORV use and the populations on the protected dunes north of Hwy. 78. We also compared the t...

Two new species of Mydidae, Rhaphiomidas pachyrhynchus sp. nov. and Rhaphiomidas moapa sp. nov. are described and illustrated here for the first time. Rhaphiomidas pachyrhynchus represents the southeastern most record of the genus. Notes on the adult ecology of R. moapa are given.

Two new species of Mydidae, Rhaphiomidas pachyrhynchus sp. nov. and Rhaphiomidas moapa sp. nov. are described and illustrated here for the first time. Rhaphiomidas pachyrhynchus represents the southeastern most record of the genus. Notes on the adult ecology of R. moapa are given.

Three chaparral plant species, Adenostoma fasciculatum Hook. and Arn. (Rosaceae), Ceanothus megacarpus Nutt. (Rhamnaceae) and Quercus berberidifolia Liebm. (Fagaceae), were sampled for micro-Hymenoptera in the Santa Rosa Plateau Nature Reserve in Southern California. Two sampling methods of the shrub's canopy are contrasted: screen-sweep netting an...

The third-instar larvae of Megasoma sleeperi Hardy are illustrated and described based upon three larval specimens. The larvae were hatched in captivity from eggs obtained from adult females collected near Glamis, Imperial Co., California, USA, in mid-September 2003. Their structure is compared with that of Megasoma occidentalis Bolivar y Pieltain...