Karen A. Ober

Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae)

The phylogeny of carabid tribes is examined with sequences of 18S ribosomal DNA from eighty‐four carabids representing forty‐seven tribes, and fifteen outgroup taxa. Parsimony, distance and maximum likelihood methods are used to infer the phylogeny. Although many clades established with morphological evidence are present in all analyses, many of the basal relationships in carabids vary from analysis to analysis. These deeper relationships are also sensitive to variation in the sequence alignment under different alignment conditions. There is moderate evidence against the monophyly of Migadopini + Amarotypini, Scaritini + Clivinini, Bembidiini and Brachinini. Psydrini are not monophyletic, and consist of three distinct lineages (Psydrus, Laccocenus and a group of austral psydrines, from the Southern Hemisphere consisting of all the subtribes excluding Psydrina). The austral psydrines are related to Harpalinae plus Brachinini. The placements of many lineages, including Gehringia, Apotomus, Omophron, Psydrus and Cymbionotum, are unclear from these data. One unexpected placement, suggested with moderate support, is Loricera as the sister group to Amarotypus. Trechitae plus Patrobini form a monophyletic group. Brachinini probably form the sister group to Harpalinae, with the latter containing Pseudomorpha, Morion and Cnemalobus. The most surprising, well supported result is the placement of four lineages (Cicindelinae, Rhysodinae, Paussinae and Scaritini) as near relatives of Harpalinae + Brachinini. Because these four lineages all have divergent 18S rDNA, and thus have long basal branches, parametric bootstrapping was conducted to determine if their association and placement could be the result of long branch attraction. Simulations on model trees indicate that, although their observed association might be due to long branch attraction, there was no evidence that their placement near Harpalinae could be so explained. These simulations also suggest that 18S rDNA might not be sufficient to infer basal carabid relationships.

Opinions on Multiple Sequence Alignment, and an Empirical Comparison of Repeatability and Accuracy between POY and Structural Alignment

An extensive literature, special symposia, and even a formal organization (International Society for Phylogenetic Nomenclature) have been devoted to various other taxonomic proposals some of which seem far more radical and/or less utilitarian than the timeclip proposal advanced here. Thus, we now invite open discussion on the temporal-banding strategy and on timeclip-like tactics that could greatly enrich existing taxonomies while still maintaining established Linnaean traditions and nomenclatures.

Phylogenetic relationships of the carabid subfamily Harpalinae (Coleoptera) based on molecular sequence data

The carabid subfamily Harpalinae contains most of the species of carabid beetles. This subfamily, with over 19,000 species, radiated in the Cretaceous to yield a large clade that is diverse in morphological form and ecological habit. While there are several morphological, cytological, and chemical characters that unite most harpalines, the placement of some tribes within the subfamily remains controversial, as does the sister group relationships to this large group. In this study, DNA sequences from the 28S rDNA gene and the wingless nuclear protein-coding gene were collected from 52 carabid genera representing 31 harpaline tribes in addition to more than 21 carabid outgroup taxa to reconstruct the phylogeny of this group. Molecular sequence data from these genes, along with additional data from the 18S rDNA gene, were analyzed with a variety of phylogenetic analysis methods, separately for each gene and in a combined data approach. Results indicated that the subfamily Harpalinae is monophyletic with the enigmatic tribes of Morionini, Peleciini, and Pseudomorphini included within it. Brachinine bombardier beetles are closely related to Harpalinae as they form the sister group to harpalines or, in some analyses, are included within it or with austral psydrines. The austral psydrines are the sister group to Harpalinae+Brachinini clade in most analyses and austral psydrines+Brachinini+Harpalinae clade is strongly supported.

Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae)

The beetle suborder Adephaga is traditionally divided into two sections on the basis of habitat, terrestrial Geadephaga and aquatic Hydradephaga. Monophyly of both groups is uncertain, and the relationship of the two groups has implications for inferring habitat transitions within Adephaga. Here we examine phylogenetic relationships of these groups using evidence provided by DNA sequences from all four suborders of beetles, including 60 species of Adephaga, 4 Archostemata, 3 Myxophaga, and 10 Polyphaga. We studied 18S ribosomal DNA and 28S ribosomal DNA, aligned with consideration of secondary structure, as well as the nuclear protein‐coding gene wingless. Independent and combined Bayesian, likelihood, and parsimony analyses of all three genes supported placement of Trachypachidae in a monophyletic Geadephaga, although for analyses of 28S rDNA and some parsimony analyses only if Coleoptera is constrained to be monophyletic. Most analyses showed limited support for the monophyly of Hydradephaga. Outside of Adephaga, there is support from the ribosomal genes for a sister group relationship between Adephaga and Polyphaga. Within the small number of sampled Polyphaga, analyses of 18S rDNA, wingless, and the combined matrix supports monophyly of Polyphaga exclusive of Scirtoidea. Unconstrained analyses of the evolution of habitat suggest that Adephaga was ancestrally aquatic with one transition to terrestrial. However, in analyses constrained to disallow changes from aquatic to terrestrial habitat, the phylogenies imply two origins of aquatic habit within Adephaga.

Phylogenetic relationships of tribes within Harpalinae (Coleoptera: Carabidae) as inferred from 28S ribosomal DNA and the wingless gene.

Abstract Harpalinae is a large, monophyletic subfamily of carabid ground beetles containing more than 19,000 species in approximately 40 tribes. The higher level phylogenetic relationships within harpalines were investigated based on nucleotide data from two nuclear genes, wingless and 28S rDNA. Phylogenetic analyses of combined data indicate that many harpaline tribes are monophyletic, however the reconstructed trees showed little support for deeper nodes. In addition, our results suggest that the Lebiomorph Assemblage (tribes Lebiini, Cyclosomini, Graphipterini, Perigonini, Odacanthini, Lachnophorini, Pentagonicini, Catapiesini and Calophaenini), which is united by a morphological synapomorphy, is not monophyletic, and the tribe Lebiini is paraphyletic with respect to members of Cyclosomini. Two unexpected clades of tribes were supported: the Zuphiitae, comprised of Anthiini, Zuphiini, Helluonini, Dryptini, Galeritini, and Physocrotaphini; and a clade comprised of Orthogoniini, Pseudomorphini, and Graphipterini. The data presented in this study represent a dense sample of taxa to examine the molecular phylogeny of Harpalinae and provide a useful framework to examine the origin and evolution of morphological and ecological diversity in this group.

ARBOREALITY AND MORPHOLOGICAL EVOLUTION IN GROUND BEETLES (CARABIDAE: HARPALINAE): TESTING THE TAXON PULSE MODEL

Abstract.— One‐third to two‐thirds of all tropical carabids, or ground beetles, are arboreal, and evolution of arboreality has been proposed to be a dead end in this group. Many arboreal carabids have unusual morphological features that have been proposed to be adaptations for life on vegetation, including large, hemispheric eyes; an elongated prothorax; long elytra; long legs; bilobed fourth tarsomeres; adhesive setae on tarsi; and pectinate claws. However, correlations between these features and arboreality have not been rigorously tested previously. I examined the evolution of arboreality and morphological features often associated with this habitat in a phylogenetic context. The number and rates of origins and losses of arboreality in carabids in the subfamily Harpalinae were inferred with parsimony and maximum‐likelihood on a variety of phylogenetic hypotheses. Correlated evolution in arboreality and morphological characters was tested with concentrated changes tests, maximum‐likelihood, and independent contrasts on optimal phylogenies. There is strong evidence that both arboreality and the morphological features examined originated multiple times and can be reversed, and in no case could the hypothesis of equal rates of gains and losses be rejected. Several features are associated with arboreality: adhesive setae on the tarsi, bilobed tarsomeres, and possibly pectinate claws and an elongated prothorax. Bulgy eyes, long legs, and long elytra were not correlated with arboreality and are probably not arboreal adaptations. The evolution of arboreal carabids has not been unidirectional. These beetles have experienced multiple gains and losses of arboreality and the morphological characters commonly associated with the arboreal habitat. The evolutionary process of unidirectional character change may not be as widespread as previously thought and reversal from specialized lifestyles or habitats may be common.

Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae)

Abstract The phylogeny of ground beetles of supertribe Trechitae is inferred using DNA sequences of genes that code for 28S ribosomal RNA, 18S ribosomal RNA, and wingless. Within the outgroups, austral psydrines are inferred to be monophyletic, and separate from the three genera of true Psydrina (Psydrus, Nomius, Laccocenus); the austral psydrines are formally removed from Psydrini and are treated herein as their own tribe, Moriomorphini Sloane. All three genes place Gehringia with Psydrina. Trechitae is inferred to be monophyletic, and sister to Patrobini. Within trechites, evidence is presented that Tasmanitachoides is not a tachyine, but is instead a member of Trechini. Perileptus is a member of subtribe Trechodina. Against Erwin’s hypothesis of anillines as a polyphyletic lineage derived from the tachyine genus Paratachys, the anillines sampled are monophyletic, and not related to Paratachys. Zolini, Pogonini, Tachyina, and Xystosomina are all monophyletic, with the latter two being sister groups. The relationships of the subtribe Bembidiina were studied in greater detail. Phrypeus is only distantly related to Bembidion, and there is no evidence from sequence data that it belongs within Bembidiina. Three groups that have been recently considered to be outside of the large genus Bembidion are shown to be derived members of Bembidion, related to subgroups: Cillenus is related to the Ocydromus complex of Bembidion, Zecillenus is related to the New Zealand subgenus Zeplataphus, and Hydrium is close to subgenus Metallina. The relationships among major lineages of Trechitae are not, however, resolved with these data.

The evolution and age of populations of Scaphinotus petersi Roeschke on Arizona Sky Islands (Coleoptera, Carabidae, Cychrini).

Abstract Populations of the ground beetle Scaphinotus petersi are isolated in subalpine conifer forest habitats on mountain ranges or Sky Islands in southeastern Arizona. Previous work on this species has suggested these populations have been isolated since the last post-glacial maximum times as warming caused this cool adapted species to retreat to high elevations. To test this hypothesis, we inferred the phylogeny from mitochondrial DNA sequence data from several Arizona Sky Island populations of Scaphinotus petersi and estimated the divergence time of the currently isolated populations. We found two major clades of Scaphinotus petersi, an eastern clade and a western group. Our results indicated most mountain ranges form clades except the Huachucas, which are polyphyletic and the Santa Catalinas, which are paraphyletic. We estimated the Pinaleño population is much older than the last glacial maximum, but the Huachuca and Pinal populations may have been fragmented from the Santa Catalina population since the post-glacial maximum times.

Rediscovery and conservation status of six short‐range endemic Pseudanophthalmus cave beetles (Carabidae: Trechini)

The North American endemic cave beetle genus Pseudanophthalmus is exceptionally diverse, with >150 described taxa in karst regions of the eastern United States. Eighty‐seven per cent of taxa, however, are at risk of extinction due to small, restricted distributions, low abundance, and several potential anthropogenic threats to their habitats. Six species in Tennessee are exceedingly rare and are candidates for listing under the U.S. Endangered Species Act: Coleman Cave Beetle (P. colemanensis), Fowlers Cave Beetle (P. fowlerae), Inquirer Cave Beetle (P. inquisitor), Bakers Station Cave Beetle (P. insularis), Nobletts Cave Beetle (P. paulus), and Soothsayer Cave Beetle (P. tiresias). Each species is an extreme short‐range endemic. Four species have not been observed in several decades, and two species (P. insularis and P. paulus) are considered possibly extinct. We searched 57 caves in 15 counties in Tennessee, including eight of the nine historical localities of the six Pseudanophthalmus species between July 2013 and March 2016 to determine if populations were still extant, to search for new populations, and to estimate relative abundance. We confirmed the continued existence of all six species, including P. fowlerae, P. insularis, P. paulus, and P. tiresias, which had not been observed in 52, 60, 50, and 42 years, respectively. We also discovered five new populations in total, one for each species except for P. paulus. Although U.S. Fish and Wildlife Service ruled that all six species do not warrant federal listing, all species continue to have restricted ranges and remain at an elevated risk of extinction.