Diversity,phylogeny and biogeography of Systomus (Teleostei,Cyprinidae) in Sri Lanka

The South and South-East Asian freshwater fish genus Systomus (Cyprinidae) comprises 17 valid species. Six nominal species, including three endemics, have been reported from Sri Lanka, a continental island separated from India by a shallow-shelf sea. The species diversity of Systomus on the island has until now not been assessed; neither has an evaluation been made of their phylogenetic history. Here, based on an analysis of the nuclear recombination activating protein 1 (rag1), and mitochondrial cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) gene markers, and a morphological examination of 143 specimens from 49 locations in Sri Lanka, we reassess the diversity of Systomus on the island and analyse patterns of their evolution and biogeography. Divergence-time estimates, based on a substitution rate calibration, date the basal split between Systomus and its sister group, the Afrotropical small barbs, to 30.0 Ma (95% highest posterior density: 25.4–35.2 Ma). The species of Systomus belong to two distinct clades. The first includes the Sri Lankan endemics S. asoka, S. martenstyni and S. pleurotaenia, which comprise an insular diversification following the immigration of a common ancestor during the Oligocene. The second, which includes the remaining species of Indian, Sri Lankan and South-East Asian Systomus, has a crown age dating to the Late Miocene. Morphological and molecular species delimitation analyses failed to validate the two nominal species, S. spilurus and S. timbiri, previously reported from Sri Lanka: both are considered synonyms of S. sarana, as are the nomina S. chryseus, S. chrysopoma, S. laticeps, S. rufus, S. pinnauratus and S. subnasutus. Four genetically and geographically discrete lineages of S. sarana occur in the island, and three in India. Molecular species delimitation analysis suggests these all belong to a single species, S. sarana. The genetically distinct Sri Lankan populations of S. sarana result from Plio-Pleistocene dispersal or vicariance events between India and Sri Lanka—as a result of emergence and inundation of the now submerged isthmus connecting the two landmasses—as well as autochthonous insular diversification.     

Multiple nuclear and mitochondrial DNA sequences provide new insights into the phylogeny of South African Lacertids (Lacertidae,Eremiadinae)

Eremiadinae, one of three subfamilies of Lacertidae, are distributed throughout Asia and Africa. Previous phylogenetic studies suggested that one of the main groups of Eremiadinae (the Ethiopian clade) consist of two clades with predominately East‐African and South‐African distribution. Yet, especially the latter one, which includes the genera Pedioplanis, Meroles, Ichnotropis, Tropidosaura and Australolacerta, was not well supported in the molecular phylogenetic analysis. In this study, we analysed the phylogenetic relationships among the genera of the ‘South African clade’ to assess whether this group actually forms a highly supported clade and to address questions concerning the monophyly of the genera. We sequenced sections of the widely used mitochondrial genes coding for 16S rRNA, 12S rRNA and cytochrome b (altogether 2045 bp) as well as the nuclear genes c‐mos, RAG‐1, PRLR, KIF24, EXPH5 and RAG‐2 (altogether 4473 bp). The combined data set increased the support values for several nodes considerably. Yet, the relationships among five major lineages within the ‘South African clade’ are not clearly resolved even with this large data set. We interpret this as a ‘hard polytomy’ due to fast radiation within the South African lacertids. The combined tree based on nine marker genes provides strong support for the ‘South African Clade’ and its sister group relationship with the ‘East African Clade’. Our results confirm the genus Tropidosaura as a monophylum, while Ichnotropis is paraphyletic in our trees: Ichnotropis squamulosa appears more closely related to Meroles than to Ichnotropis capensis. Furthermore, the monophyly of Meroles is questionable as well. Based on our results, I. squamulosa should be transferred from Ichnotropis into the genus Meroles. Also, the two species of Australolacerta (A. australis and A. rupicola) are very distantly related and the genus is perhaps paraphyletic, too. Finally we propose a phylogeographical scenario in the context of palaeoclimatic data and compare it with a previously postulated hypothesis.     

Multiple origins of polyploidy in the phylogeny of southern African barbs (Cyprinidae) as inferred from mtDNA markers

The cyprinid genus Barbus, with more than 800 nominal species, is an apparently polyphyletic assemblage to which a number of unrelated species, groups and/or assemblages have been assigned. It includes species that exhibit three different ploidy levels: diploid, tetraploid and hexaploid. Several lineages of the family Cyprinidae constitute a major component of the African freshwater ichthyofauna, having about 500 species, and fishes assigned to the genus 'Barbus' have the most species on the continent. We used complete sequences of the mitochondrial cytochrome b gene in order to infer phylogenetic relationships between diploid, tetraploid and hexaploid species of 'Barbus' occurring in southern Africa, the only region where representatives of all of the three ploidy levels occur. The results indicate that most of the lineages are incorrectly classified in the genus 'Barbus'. The southern African tetraploids probably originated from southern African diploids. They constitute a monophyletic group distinct from tetraploids occurring in the Euro-Mediterranean region (Barbus sensu stricto). The 'small' African diploid species seem to be paraphyletic, while the 'large' African hexaploid barbs species are of a single, recent origin and form a monophyletic group. The evidence of multiple, independent origins of polyploidy occurring in the African cyprinine cyprinids thus provides a significant contribution to the knowledge on the systematic diversity of these fishes, and warrants a thorough taxonomic reorganization of the genus.     

The phylogenetic affinities of the Socotra Bunting Emberiza socotrana

The monophyly of the African ‘brown bunting’ complex was corroborated by a recent molecular study. However, the little-known Socotran endemic Emberiza socotrana, which is morphologically similar to the other taxa in this complex, was not included. Here we present a hypothesis of the phylogenetic relationships of the Socotra Bunting based on one mitochondrial gene and one nuclear intron. We found the Socotra Bunting to be deeply nested within the African ‘brown bunting’ complex and, although morphologically most similar to E. capensis, it proved to be more closely related to the E. striolata/sahari and E. tahapisi/goslingi species groups. The phylogenetic uniqueness of the Socotra Bunting underpins once more the evolutionary importance of the Endemic Bird Area of Socotra, which is often considered the ‘Galápagos of the Indian Ocean’.     

Evolutionary history and speciation modes in the cyprinid genus Barbus.

Phylogenetic relationships and evolutionary patterns in the genus Barbus were examined through the analysis of the complete sequences of three mitochondrial genes: ATPases 8 and 6, which overlap slightly, and cytochrome b. This complex genus includes diploid as well as tetraploid and hexaploid species that are distributed throughout the Palaearctic, Ethiopian and Asiatic biogeographical regions. Given that genome duplication is an important evolutionary mechanism in eukaryotes, in the present report we attempt to describe its role in the evolution of the genus Barbus, as well as drawing systematic and phylogenetic conclusions. The phylogenetic results indicated the splitting of the current Barbus genus into five main mitochondrial lineages corresponding to (i) the genus Barbus sensu stricto (tetraploid, which is subdivided into the subgenera Barbus and Luciobarbus), (ii) the hexaploid species, (iii) the Ethiopian tetraploid species, (iv) the African diploid species, and (v) the Asian diploid species. The branching of 'foreign' genera as sister groups of some of these monophyletic assemblages (such as Aulopyge is to Barbus sensu stricto or Varicorhinus is to the hexaploid barbels) demonstrates the polyphyly of the group. Moreover, the relationships between the proposed lineages also show that genome duplication may be considered as a homoplasic character since it must have occurred over at least three independent periods and/or in three independent areas. In relation to the possible saltational evolutionary model for the polyploid species examined here, it was found that, although feasible at the nuclear level, the mitochondrial markers looked at do not appear to have undergone this type of evolution. Rather, they seem to have experienced more or less constant change through time.     

Diploid-tetraploid relationship among old-world members of the fish family Cyprinidae

Evidence suggesting that the goldfish and the carp of the family Cyprinidae are tetraploid species in relation to other members of the same family were presented. The two barb species, Barbus tetrazona and Barbus jasciatus, were chosen as representatives of diploid members of the family Cyprinidae. These barbs had the diploid chromosome number of 50 and 52 and the DNA value 20–22% that of placental mammals, while the goldfish (Carassius auratus) and the carp (Cyprinus carpio) had the diploid chromosome number of about 104 and the DNA value 50–52% that of placental mammals.Supported in part by a grant (CA-05138) from the National Cancer Institute, U.S.Public Health Service, and in part by a research fund established in honor of General James H. Doolittle at Duarte, and by the British Empire Cancer Campaign for Research at Northwood. Contribution No. 11-67, Department of Biology, City of Hope Medical Center. Dr. Junichi Muramoto is a fellow of the Institute for Advanced Learning of the City of Hope Medical Center.     

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

Abstract The diploid Oryza species with C‐genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C‐genome (BBCC, CCDD). Despite extensive studies, the phylogenetic relationship among the C‐genome species and the taxonomic status of some taxa remain controversial. In this study, we reconstructed the phylogeny of three diploid species with C‐genome (Oryza officinalis, O. rhizomatis, and O. eichingeri) based on sequences of 68 nuclear single‐copy genes. We obtained a fully resolved phylogenetic tree, clearly indicating the sister relationship of O. officinalis and O. rhizomatis, with O. eichingeri being the more divergent lineage. Incongruent phylogenies of the C‐genome species found in previous studies might result from lineage sorting, introgression/hybridization and limited number of genetic markers used. We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O. eichingeri. Analyses of two datasets (68 genes with a single sample, and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O. eichingeri. In addition, we evaluated the impact of the number of sampled individuals and loci on species delimitation. Our simulation suggests that sampling multiple individuals is critically important for species delimitation, particularly for closely related species.     

Growth, biomass, and production of two small barbs (Barbus humilis and B. tanapelagius, Cyprinidae) and their role in the food web of Lake Tana (Ethiopia)

Growth, biomass and production of two small barbs (Barbus humilis and Barbus tanapelagius) and their role in the food web of Lake Tana were investigated. From length–frequency distribution of trawl monitoring surveys growth coefficient, Φ′ values were estimated at 3.71–4.17 for B. humilis and 3.70–4.14 for B. tanapelagius, respectively. Values for B. humilis were confirmed in pond experiments. Mean biomass of the small barbs was 13.3 kg fresh wt ha⁻¹, with B. humilis being most abundant in the littoral and sub-littoral zones, whereas B. tanapelagius was most abundant in the sub-littoral and pelagic zones. The two small barbs had a production of 53 kg fresh wt ha⁻¹ year⁻¹. Although their P/B ratios of about 4.0 were relatively high for small cyprinids, both their biomass and production were low in comparison with other small fish taxa in other tropical lakes. Of the zooplankton production only about 29% was consumed by the small barbs. However, they did not utilize calanoid copepods, which were responsible for approximately 57% of the zooplankton production and it is likely that small barb production was food limited during certain periods of the year. Piscivorous labeobarbs consumed about 56% of the small barbs production annually, but additionally, Clarias gariepinus, and many bird species were also preying on them. Therefore, limitation of Barbus production by predation during certain periods in the year cannot be excluded.     

Phylogenetic position and composition of Zygiellinae and Caerostris,with new insight into orb‐web evolution and gigantism

Orb‐weaving spiders are good objects for evolutionary research, but phylogenetic relationships among and within orb‐weaving lineages are poorly understood. Here we present the first species‐level molecular phylogeny that includes the enigmatic orb weavers ‘Zygiellidae’ and Caerostris. Zygiellidae is interesting for the evolution of the sector web, and Caerostris is noteworthy for web gigantism and extraordinary silk biomechanics. We assembled a molecular data set using mitochondrial (COI, 16S) and nuclear (H3, 18S, 28S, ITS2) gene fragments for 112 orbicularian exemplars, focusing on taxa with diverse web architecture and size. We show that ‘Zygiellidae’ contains the Holarctic Zygiella genus group (Leviellus, Parazygiella, Stroemiellus, and Zygiella) and the Australasian Phonognatha and Deliochus. As this clade is placed with Araneidae in all analyses we treat it as a subfamily, Zygiellinae. Using the new phylogeny, we show that the sector web evolved eight times, and coevolved with the silk tube retreat, but that these features are not zygielline synapomorphies. Zygiellinae, Caerostris, and some other araneids form a basal grade of araneids that differ from ‘classical’ araneids in web‐building and preying behaviour. We also confirm that Caerostris represents the most striking case of spider‐web gigantism. © 2015 The Linnean Society of London     

An underground burst of diversity – a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Using both nuclear and mitochondrial sequences, we demonstrate high genetic differentiation in the genus Talpa and confirm the existence of cryptic species in the Caucasus and Anatolia, namely, T. talyschensis Vereschagin, 1945, T. ognevi Stroganov, 1948, and Talpa ex gr. levantis. Our data support four clades in the genus Talpa that showed strong geographical associations. The ‘europaea’ group includes six species from the western portion of the genus' range (T. europaea, T. occidentalis, T. romana, T. caeca, T. stankovici, and T. levantis s.l.); another three groups are distributed further east: the ‘caucasica’ group (Caucasus), the ‘davidiana’ group (eastern Anatolia and Elburz) and T. altaica (Siberia). The phylogenetic position of T. davidiana was highlighted for the first time. The order of basal branching remains controversial, which can be attributed to rapid diversification events. The molecular time estimates based on nuclear concatenation estimated the basal divergence of the crown Talpa during the latest Miocene. A putative scenario of Talpa radiation and issues of species delimitation are discussed. © 2015 The Linnean Society of London     

Morphology, molecules, and character congruence in the phylogeny of South American geophagine cichlids (Perciformes, Labroidei)

Phylogenetic relationships among the Neotropical cichlid subfamily Geophaginae were examined using 136 morphological characters and a molecular dataset consisting of six mitochondrial and nuclear genes. Topologies produced by morphological and combined data under parsimony were contrasted, congruence among different partitions was analysed, and potential effects of character incongruence and patterns of geophagine evolution on phylogenetic resolution are discussed. Interaction of morphological and molecular characters in combined analysis produced better resolved and supported topologies than when either was analysed separately. Combined analyses recovered a strongly supported Geophaginae that was closely related to Cichlasomatinae. Within Geophaginae, two sister clades included all geophagine genera. Acarichthyini (Acarichthys+Guianacara) was sister to the ‘B clade’, which contained the ‘Geophagus clade’ (‘Geophagus’steindachneri+Geophagus sensu stricto, and both sister to Gymnogeophagus) as sister to the ‘Mikrogeophagus clade’ (Mikrogeophagus+‘Geophagus’brasiliensis), and in turn, the Geophagus and Mikrogeophagus clades were sister to the crenicarine clade (Crenicara+Dicrossus) and Biotodoma. The second geophagine clade included the ‘Satanoperca clade’ (Satanoperca+Apistogramma and Taeniacara) as sister to the ‘Crenicichla clade’ (Crenicichla+Biotoecus). Several lineages were supported by unique morphological synapomorphies: the Geophaginae + Cichlasomatinae (5 synapomorphies), Geophaginae (1), Crenicichla clade (3), crenicarine clade (1), the sister relationship of Apistogramma and Taeniacara (4) and of Geophagus sensu stricto and‘Geophagus’steindachneri (1), and the cichlasomine tribe Heroini (1). Incorporation of Crenicichla in Geophaginae reconciles formerly contradictory hypotheses based on morphological and molecular data, and makes the subfamily the most diverse and ecologically versatile clade of cichlids outside the African great lakes. Results of this study support the hypothesis that morphological differentiation of geophagine lineages occurred rapidly as part of an adaptive radiation.     

Phenetic relationships and probable ways of morphological diversification of the African large barbs (<Emphasis Type="Italic">Barbus intermedius</Emphasis> complex) in Lake Tana (Ethiopia)

29 quantitative and 18 qualitative skull characters were studied in the African large barbs (Barbus intermedius complex) from Lake Tana (Ethiopia). Based on results of principle components analysis phenetic relationships of 12 morphotypes were assessed. External features diagnostic of the morphotypes were found in individuals substantially different in the skull characters. The obtained data along with the data on morphological diversity of large barbs from Ethiopia beyond the Lake Tana basin suggest origination of the Lake Tana complex of forms from a complex of forms that existed in the upper reaches of the Blue Nile before the lake came into being, and the extant morphotypes of the Lake Tana barbs originated from three or four forms that composed the ancestral riverine local complex.     

A new species of the sclerorhynchid sawfish Borodinopristis from the Campanian (Upper Cretaceous) of North Carolina,USA

Elasmobranch fossils recovered from Campanian marine exposures at Elizabethtown, Bladen County, NC, include species from at least seven genera of sharks and four genera of batoids. Of particular interest is the recovery of multiple isolated rostral spines from a new sclerorhynchid sawfish, Borodinopristis shannoni, sp. nov. Species of Borodinopristis are known from oral teeth and/or rostral spines (‘rostral teeth’ for some authors). In species known from the latter, the spines differ from those of other sclerorhynchids by the presence of one or more ‘collared’ barbs on the posterior margin of the crown. Unlike the previously described B. schwimmeri, the rostral spines of the new species have well-developed hooked barbs with collars (curved, connected crests) extending asymmetrically onto the dorsal and ventral surfaces of the spine, as well as small, rudimentary barbs. Also unlike B. schwimmeri, the anterior margin of the spine is strongly convex and there is no enamelled collar at the base of the crown. The new species also occurs in the Upper Cretaceous of the Gulf Coastal Plain.     

Polymorphism of skull proportions in large African barbs <Emphasis Type="Italic">Barbus intermedius</Emphasis> sensu Banister (Cyprinidae) from Lakes Awasa and Langano (Rift Valley,Ethiopia)

After performing principal component analysis (PCA) of 13 characters (indices) of skulls of large African barbs (Barbus intermedius complex sensu Banister, 1973) from Lakes Awasa and Langano (Ethiopia) distributions of individuals in coordinates BL and PC1 were studied where BL is the basal skull length and PC1 is the first principal component. It is shown that in both the lakes there are groups of barbs whose individual ontogenetic trajectories are situated within separated ontogenetic channels. Separation of the channels is by far less distinct than that of the channels of generalized and specialized forms of barbs from Lake Tana and not correlated with differences in external traits. It is suggested that the revealed polymorphism is connected with food resource partitioning and might serve as a prerequisite of further divergence of sympatric forms of large African barbs.     

A reappraisal of the genus Megacaryon (Boraginaceae,Lithospermeae) based on molecular,morphological, and karyological evidence

The systematic position and phylogenetic relationships of Echium orientale, a rare endemic of the mountains of northern Turkey, were elucidated based on morphological, molecular, and karyological evidence.

Using nuclear and plastid DNA sequences, we found that this species is not included in Echium, but is rather at least as divergent from it as other related lineages, namely the South African Lobostemon and Echiostachys. Pollen characters revealed a strong affinity with Onosma, especially in the non-reticulate ornamentation of the tectum. Fruit morphology is unique in the genera of the Echium ‘alliance' (e.g. Echium, Pontechium, Lobostemon, and Echiostachys), because of the large size and the smooth, glossy nutlet surface as in most species of Onosma. Karyological observations show that this species is diploid with 2n = 12, and differing from both Lobostemon or Echium, where nearly all species have higher numbers (usually 2n = 14 and 2n = 16, respectively). Combined with a ‘megaherb' habit, the weak zygomorphism of the large flowers and a restricted range in the humid mountain forests of the Black Sea region, fruit, pollen and chromosome characters suggest an isolated position for E. orientale in the Echium alliance. We therefore propose its placement in the monotypic Megacaryon, a genus originally described by Boissier, but largely disregarded by later botanists. An original specimen is designated as generic lectotype.     

What haplodiploids can teach us about hybridization and speciation

Most evolutionary theory focuses on species that reproduce through sexual reproduction where both sexes have a diploid chromosome count. Yet a substantial proportion of multicellular species display complex life cycles, with both haploid and diploid life stages. A classic example is haplodiploidy, where females develop from fertilized eggs and are diploid, while males develop from unfertilized eggs and are haploid. Although haplodiploids make up about 15% of all animals (de la Filia et al. 2015 ), this type of reproduction is rarely considered in evolutionary theory. In this issue of Molecular Ecology, Patten et al. ( 2015 ) develop a theoretical model to compare the rate of nuclear and mitochondrial introgression in haplodiploid and diploid species. They show that when two haplodiploid species hybridize, nuclear genes are much less likely to cross the species barrier than if both species were to be diploids. The reason for this is that only half of the offspring resulting from matings between haplodiploid species are true hybrids: sons from such mating only inherit their mother genes and therefore only contain genes of the maternal species. Truly, hybrid males can only occur through backcrossing of a hybrid female to a male of one of the parental species. While this twist of haplodiploid transmission genetics limits nuclear introgression, mitochondrial genes, which are maternally inherited, are unaffected by the scarcity of hybrid males. In other words, the rate of mitochondrial introgression is the same for haplodiploid and diploid species. As a result, haplodiploid species on average show a bias of mitochondrial compared to nuclear introgression.     

Combining geometric morphometrics with molecular genetics to investigate a putative hybrid complex: a case study with barbels Barbus spp. (Teleostei: Cyprinidae)

This integrative study examined the morphological and genetic affinities of three endemic barbel species from Italy (brook barbel Barbus caninus, Italian barbel Barbus plebejus and horse barbel Barbus tyberinus) and of putative hybrid specimens to their species of origin. Two of the species frequently occur together with the non‐native barbel Barbus barbus. DNA barcoding indicates that mitochondrial (mt) haplotypes often do not match the species expected from morphology. Linear distance measurements and meristics are not informative for discrimination of the species and putative hybrids, but a discriminant analysis of principal components (DAPC) of geometric landmark data produces reassignments largely in congruence with mt and nuclear genetic data. Cyto‐nuclear conflicts confirm the presence of hybridization in B. plebejus and B. tyberinus and identify additional introgressed specimens. A comparison between mixed genotypes and their morphology‐based assignment reveals no predictable pattern. The finding that most individuals of the morphologically similar B. plebejus and B. tyberinus have very high assignment probabilities to their respective species suggests that the presented approach may serve as a valuable tool to distinguish morphologically very similar taxa.