Deep Molecular Divergence Research Articles

Genetic diversity, phylogenetic position and morphometric analysis of Astacus colchicus (Decapoda, Astacidae): a new insight into Eastern European crayfish fauna.

The phylogeny of European crayfish fauna, especially with respect to Eastern European species, is still far from being completely resolved. To fill this gap, we analyzed most of the European crayfish species focusing on the phylogenetic position of the endemic crayfish Astacus colchicus, inhabiting Georgia. Three mitochondrial and one nuclear marker were used to study evolutionary relationships among European crayfish species, resulting in the unique phylogenetic position of A. colchicus indicating independent species status to A. astacus. Phylogenetic analyses revealed a deep molecular divergence of A. colchicus in comparison to A. astacus (6.5-10.9% in mtDNA and 1.1% in nDNA) as well as to Pontastacus leptodactylus and P. pachypus (5.5-10.0% in mtDNA and 1.4-2.4% in nDNA). Absent ventral process on second male pleopod and abdominal somites II and III with pleura rounded lacking prominent spines clearly indicate taxonomic assignment to the genus Astacus; however, the species is distributed almost in the middle of Ponto-Caspian area typical by occurrence of the genus Pontastacus. Several morphological indices linked to head length, carapace, and total body length and width were found to demonstrate apparent differences between A. colchicus and A. astacus. Although this study provides a novel insight into European crayfish phylogeography, we also point out the gaps in comprehensive study of the P. leptodactylus species complex, which could reveal details about the potential species status of particular species and subspecies within this genus.

Deep molecular divergence and exceptional morphological stasis in dwarf cannibal snails Nata sensu lato Watson, 1934 (Rhytididae) of southern Africa

The genus Nata Watson, 1934 is a southern African endemic belonging to the Gondwanan family of carnivorous snails, Rhytididae. We present a molecular phylogeny of the genus based on two mitochondrial (16S and COI) and two nuclear genes (ITS2 and 28S RNA), and complement this with an appraisal of morphological characters relating to both the shell and soft parts. We identify four reciprocally monophyletic lineages for which valid names are already available, plus two undescribed species restricted to the Albany Thicket Biome. We show that Nata sensu lato may not be monophyletic. Rather there exist two deep lineages within Nata s.l., one lineage potentially sister to a clade dominated by the Australian and New Zealand radiation, and the other occupying a basal position within Rhytididae. Accordingly we recommend a revision recognising two genera, namely Nata s.s. and Natella respectively. Despite deep molecular divergences within Nata s.s., phenotypic evolution has been remarkably conserved, and contrasts greatly with that exhibited across other major lineages within the Rhytididae.

English

We describe a new species of agamid lizard, Ctenophorus mirrityana sp.nov. currently known from two disjunct populations in western New South Wales. The species is a member of the C. decresii species complex, and was formerly recognized as an outlying population of C. decresii due to similarities in dorsal colour pattern and adjacent distributions. Previous work documented deep molecular divergence, across multiple loci, with no genetic admixture between the new species and proximal C. decresii populations. We find that the new species differs in morphology from all other members of the species complex and is characterized by distinct male throat and lateral coloration, a small head size relative to snout-vent length, a large number of labial scales, and a lack of tubercular scales. We also identify two geographically structured lineages (northern and southern) within C. decresii as requiring further taxonomic investigation, based on notable genetic and morphological (including colour) divergence. We find that divergence in coloration is associated with genetic and body form differentiation within the C. decresii species complex.

Water barriers and intra‐island isolation contribute to diversification in the insular Aethopyga sunbirds (Aves: Nectariniidae)

AbstractAimColonization and subsequent isolation across deep‐water barriers is thought to be the primary driver of diversification in insular birds. Shallow‐water barriers and intra‐island isolation are less well‐documented drivers of avian diversification. We examined the relative roles of different geographical barriers in the diversification of Aethopyga sunbirds, a widespread Southeast Asian genus that has its greatest diversity in the Philippine Archipelago.LocationPhilippines, Southeast Asia, Wallacea.MethodsWe reconstructed the phylogenetic relationships among Aethopyga sunbirds with mitochondrial and nuclear DNA sequences. Phylogeny was inferred using concatenated and coalescent frameworks, implemented in maximum likelihood and Bayesian analyses. We used maximum likelihood ancestral state reconstructions to examine the ancestral distribution and colonization history of Aethopyga. To determine whether the diversification at each node occurred within a continent, across a shallow‐water barrier, across a deep‐water barrier or within an island, we used a series of statements based on the phylogeny, current distribution of species and bathymetric reconstructions.ResultsAncestral state reconstructions inferred that the core Aethopyga ancestor was continental, and that the diversity of Aethopyga on oceanic islands is the result of three or four independent colonization events. Dispersal and subsequent isolation across deep‐water barriers was the most common mode of diversification in insular Aethopyga, although intra‐island isolation contributed to diversity, producing a small montane radiation within Mindanao. Analyses inferred only a single unequivocal event of diversification across a shallow‐water barrier. Deep molecular divergences between phenotypically distinct subspecies suggested that the taxonomy of Aethopyga is overly conservative and obscures biogeographical patterns. We recommend elevating five subspecies, all of which are endemic to the Philippines, to full species.Main conclusionsIn addition to corroborating the importance of isolation across deep‐water barriers, these data also underscore a potential role for additional isolating mechanisms in the generation of biodiversity on oceanic islands. A clade of four montane Aethopyga taxa evolved in situ within the Mindanao sky‐island system, an exception to the paradigm that birds do not diversify within the geographical confines of oceanic islands.

Molecular phylogenetic, morphological and biogeographic evidence for a new genus of parabathynellid crustaceans (Syncarida : Bathynellacea) from groundwater in an ancient southern Australian landscape

The putatively ancient subterranean crustacean family Parabathynellidae has been poorly studied, in part because of the problem of obtaining material from difficult to access subterranean habitats in which they live. Further, the systematics of the group has been complicated by their generally simplified morphology and isolated descriptions of new taxa in the absence of any phylogenetic framework. Using material from comprehensive field surveys and mitochondrial cytochrome c oxidase subunit I (COI) and nuclear 18S sequence data, plus morphology, a new genus is recognised, Arkaroolabathynella Abrams & King, gen. nov., from underground waters in the Flinders Ranges, South Australia. Arkaroolabathynella contains four genetically and morphologically distinct species, described as A. bispinosa Abrams & King, sp. nov., A. remkoi Abrams & King, sp. nov., A. robusta Abrams & King, sp. nov. and A. spriggi Abrams & King, sp. nov. Phylogenetic analysis also revealed a previously unknown diversity of parabathynellids from southern Australia, and a complex set of relationships with the eastern (New South Wales) and south-western (Western Australia) continental faunas. Additionally, this study showed that deep molecular divergences in parabathynellids are not always reflected in morphological divergence. A checklist to Australian parabathynellid genera and species is also provided.

Extensive Phylogeographic and Morphological Diversity in Diporiphora nobbi (Agamidae) Leads to a Taxonomic Review and a New Species Description

Morphological and molecular information is invaluable in the description of cryptic diversity and the evolutionary processes driving diversification within closely related species that exhibit morphological homoplasy. We present a distribution-wide data set consisting of both molecular and morphological information, providing a taxonomic revision of the Diporiphora nobbi species group, and develop preliminary hypotheses regarding the evolutionary history of D. nobbi. We show deep molecular divergence between D. nobbi and a newly described sister lineage associated with divergence in meristic characters. Our molecular data also show large divergences among subclades within nominate D. nobbi associated with different habitats rather than specific biogeographc barriers. We further discuss potential diversification mechanisms within the D. nobbi species group.

Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae)

The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of the genus including multiple exemplars, together with the closely related genera Prostomoxys Zumpt, Haematobosca Bezzi, and Haematobia Lepeletier & Serville. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods from DNA fragments from the cytochrome c oxidase subunit I (COI, 753bp) and cytochrome b (CytB, 587bp) mitochondrial genes, and the nuclear ribosomal internal transcribed spacer 2 (ITS2, 426bp). The combination of mitochondrial and nuclear data strongly supports the paraphyly of the genus Stomoxys because of the inclusion of Prostomoxys saegerae Zumpt. This unexpected result suggests that Prostomoxys should be renamed into Stomoxys. Also, the deep molecular divergence observed between the subspecies Stomoxys niger niger Macquart and S. niger bilineatus Grünbreg led us to propose that they should rather be considered as distinct species, in agreement with ecological data. Bayesian phylogenetic analyses support three distinct lineages within the genus Stomoxys with a strong biogeographical component. The first lineage consists solely of the divergent Asian species S. indicus Picard which appears as the sister-group to all remaining Stomoxys species. The second clade groups the strictly African species Stomoxys inornatus Grünbreg, Stomoxys transvittatus Villeneuve, Stomoxys omega Newstead, and Stomoxys pallidus Roubaud. Finally, the third clade includes both African occurring and more widespread species such as the livestock pest Stomoxys calcitrans Linnaeus. Divergence time estimates indicate that the genus Stomoxys originated in the late Oligocene around 30 million years ago, with the major lineages diversifying in the Early Miocene between 20 and 15 million years ago at a time when temperate forests developed in the Northern Hemisphere.

Signals of recent spatial expansions in the grey mouse lemur (Microcebus murinus)

BackgroundPleistocene events have shaped the phylogeography of many taxa worldwide. Their genetic signatures in tropical species have been much less explored than in those living in temperate regions. We analysed the genetic structure of a Malagasy primate species, a mouse lemur with a wide distribution (M. murinus), in order to investigate such phylogeographic processes on a large tropical island. We also evaluated the effects of anthropogenic pressures (fragmentation/deforestation) and natural features (geographic distance, rivers) on genetic structure in order to complement our understanding of past and present processes of genetic differentiation.ResultsThe analysis of the mitochondrial D-loop sequences of 195 samples from 15 study sites (10 from a continuous forest and five from isolated forest fragments) from two adjacent Inter-River-Systems (IRSs) revealed that forest fragmentation and the river restrict gene flow, thereby leading to an increased genetic differentiation between populations beyond the effect of isolation-by-distance. Demographic simulations detected signals of two successive spatial expansions that could be preliminarily dated to the late Pleistocene and early Holocene. The haplotype network revealed geographic structure and showed deep molecular divergences within and between the IRSs that would be congruent with a two-step colonization scenario.ConclusionsThis study supports the hypothesis of a relatively recent spatial expansion of the grey mouse lemur in northwestern Madagascar, which may also explain why this taxon, in contrast to its congeners, has not yet undergone allopatric speciation in the studied area and possibly across its presently wide range.

Catchments catch all: long‐term population history of a giant springtail from the southeast Australian highlands — a multigene approach

Phylogeography can reveal evolutionary processes driving natural genetic-geographical patterns in biota, providing an empirical framework for optimizing conservation strategies. The long-term population history of a rotting-log-adapted giant springtail (Collembola) from montane southeast Australia was inferred via joint analysis of mitochondrial and multiple nuclear gene genealogies. Contemporary populations were identified using multilocus nuclear genotype clustering. Very fine-scale sampling combined with nested clade and coalescent-based analyses of sequences from mitochondrial cytochrome oxidase I and three unlinked nuclear loci uncovered marked population structure, deep molecular divergences, and abrupt phylogeographical breaks over distances on the order of tens of kilometres or less. Despite adaptations that confer low mobility, rare long-distance gene flow was implicated: novel computer simulations that jointly modelled stochasticity inherent in coalescent processes and that of DNA sequence evolution showed that incomplete lineage sorting alone was unable to explain the observed spatial-genetic patterns. Impacts of Pleistocene or earlier climatic cycles were detected on multiple timescales, and at least three putative moist forest refuges were identified. Water catchment divisions predict phylogeographical patterning and present-day population structure with high precision, and may serve as an excellent surrogate for biodiversity indication in sedentary arthropods from topographically heterogeneous montane temperate forests.

Molecular phylogeny of diploid Bulinus sp. (Gastropoda: Planorbidae) populations in Cameroon crater lakes

Bulinus sp. (2 n = 36) is a diploid freshwater snail found in Cameroon crater lakes; it belongs to a group of medically important freshwater snails. Some members ( Bulinus truncatus, Bulinus tropicus) of this group had been reported to be involved in the transmission of parasites ( Schistosoma sp. and Calicophoron microbothrium) to human and livestock in tropical Africa. Yet, understanding of the evolutionary identity of the diploid snail such as its phylogenetic position and the genetic divergence among populations, remains limited. In this study, we constructed the molecular phylogeny of Bulinus sp. using sequences of mitochondrial cytochrome oxydase subunit 1 (CO-1, 365 nucleotides). Partial sequences of CO-1 were obtained and genetic divergences between populations estimated after the alignment of 365 nucleotides from each studied population. The lack of deep molecular divergences between populations of Bulinus sp. from western Cameroon crater lakes may indicate that they belong to the same lineage; therefore, it implies that diploid B. truncatus/ tropicus complex snail-like in Cameroon share a common ancestor. The CO-1 of the three studied populations of Bulinus sp., clustered together with other diploid pan-African representatives of the B. truncatus/ tropicus complex, showed little evidence of genetic similarities.

Phylogeny ofMysis(Crustacea, Mysida): history of continental invasions inferred from molecular and morphological data

AbstractWe studied the phylogenetic history of opossum shrimps of the genusMysisLatreille, 1802 (Crustacea: Mysida) using parsimony analyses of morphological characters, DNA sequence data from mitochondrial (16S, COI and CytB) and nuclear genes (ITS2, 18S), and eight allozyme loci. With these data we aimed to resolve a long‐debated question of the origin of the non‐marine (continental) taxa in the genus, i.e., “glacial relicts” in circumpolar postglacial lakes and “arctic immigrants” in the Caspian Sea. A simultaneous analysis of the data sets gave a single tree supporting monophyly of all continental species, as well as monophyly of the taxa from circumpolar lakes and from the Caspian Sea. A clade of three circumarctic marine species was sister group to the continental taxa, whereas Atlantic species had more distant relationships to the others. Small molecular differentiation among the morphologically diverse endemic species from the Caspian Sea suggested their recent speciation, while the phenotypically more uniform “glacial relict” species from circumpolar lakes (Mysis relictagroup) showed deep molecular divergences. For the length‐variable ITS2 region both direct optimization anda priorialignment procedures gave similar topologies, although the former approach provided a better overall resolution. In terms of partitioned Bremer support (PBS), mitochondrial protein coding genes provided the largest contribution (83%) to the total tree resolution. This estimate however, appears to be partly spurious, due to the concerted inheritance of mitochondrial characters and probable cases of introgression or ancestral polymorphism.© The Willi Hennig Society 2005.

Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spiderAptostichus simus

Aptostichus simus is a trapdoor spider endemic to the coastal dunes of central and southern California and, on morphological grounds, is recognized as a single species. Mitochondrial DNA 16S rRNA sequences demonstrate that most populations are fixed for the same haplotype and that the population haplotypes from San Diego County, Los Angeles County, Santa Rosa Island, and Monterey County are extremely divergent (6-12%), with estimated separation times ranging from 2 to 6 million years. A statistical cluster analysis of morphological features demonstrates that this genetic divergence is not reflected in anatomical features that might signify ecological differentiation among these lineages. The species status of these divergent populations of A. simus depends upon the species concept utilized. If a time-limited genealogical perspective is employed, A. simus would be separated at the base into two genetically distinct species. This study suggests that species concepts based on morphological distinctiveness, in spider groups with limited dispersal capabilities, probably underestimate true evolutionary diversity.

Provenance Of Atlantic Lingulid Brachiopods

Living lingulid brachiopods are ubiquitous in low‐latitude, marine infaunas. Lingula occurs throughout the Pacific and Indian oceans with the only Atlantic species, L. parva, confined to West Africa. Glottidia is restricted to offshore America from Virginia to California and Peru, and is assumed to have descended from a Pacific Lingula during the early Tertiary. Lingulid organophosphatic shells differ structurally. That of Glottidia is characterizedby trellised rods (baculate); that of Indo‐Pacific species of Lingula by spheroidal and rod‐like microstructures (virgose); and that of L. parva by apatitic rods arranged as spherulites. A spherulitic fabric is unknown in fossil lingulids, but the distinction between GlottidiaLingula can be traced back to the Carboniferous, which accords with the deep molecular divergence between the two genera. The common occurrence of lingulids with baculate shells in European post‐Palaeozoic sediments suggests that ancestral Glottidia entered the Atlantic by the Tethyan Current during the Late Cretaceous/early Cenozoic, and migrated into the Pacific before the formation of the Panama Isthmus. Penecontemporaneously, antecedents of L. parva possibly migrated from east Tethys along the trans‐Saharan seaway.

Molecular phylogeny of the free-living archezoan Trepomonas agilis and the nature of the first eukaryote.

We have sequenced the small ribosomal subunit RNA gene of the diplozoan Trepomonas agilis. This provides the first molecular information on a free-living archezoan. We have performed a phylogenetic analysis by maximum likelihood, parsimony, and distance methods for all available nearly complete archezoan small subunit ribosomal RNA genes and for representatives of all major groups of more advanced eukaryotes (metakaryotes). These show Diplozoa as the earliest-diverging eukaryotic lineage, closely followed by microsporidia. Trepomonas proves to be much more closely related to Hexamita, and, to a lesser degree, to Spironucleus, than to Giardia. The close relationship between the free-living Trepomonas on our trees and the parasites Hexamita inflata and Spironucleus refutes the idea that the early divergence of the amitochondrial Archezoa is an artefact caused by parasitism. The deep molecular divergence between the three phagotrophic genera with two cytostomes (Hexamita, Trepomonas, Spironucleus) and the saprotrophic Giardia that lacks cytostomes is in keeping with the classical evidence for a fundamental difference in the symmetry of the cytoskeleton between the two groups. We accordingly separate the two groups as two orders: Distomatida for those with two cytostomes/cytopharynxes and Giardiida ord. nov. for Giardia and Octomitus that lack these, and divide each order into two families. We suggest that this fundamental divergence in manner of feeding and in the symmetry of the cytoskeleton evolved in a free-living diplozoan very early indeed in the evolution of the eukaryotic cell, possibly very soon after the origin of the diplokaryotic state (having two nuclei linked together firmly by the cytoskeleton) and before the evolution of parasitism by distomatids and giardiids, which may have colonized animal guts independently. We discuss the possible relationship between the two archezoan phyla (Metamonada and Microsporidia) and the nature of the first eukaryotic cell in the light of our results and other recent molecular data.