The molecular systematics of Leiopotherapon unicolor (Günther, 1859): testing for cryptic speciation in Australia's most widespread freshwater fish

Leiopotherapon unicolor is the most widespread freshwater fish species in Australia. A comprehensive allozyme and mitochondrial DNA 16S rRNA data set was assembled from 141 specimens of L. unicolor collected Australia-wide in order to test for cryptic speciation in this far-ranging species. Surprisingly, little genetic diversity was observed within L. unicolor and provided no evidence for the existence of cryptic species within this lineage. In contrast, a small sample set of L. aheneus used as the outgroup showed two highly divergent haplotypes strongly suggestive of cryptic speciation. L. unicolor has a number of ecological and life history attributes that may explain the lack of significant genetic divergence over substantial geographical distances. The occurrence of other widespread fish and crustacean species that also display only limited genetic diversity indicate that climate conditions more favourable to dispersal across central and northern Australia than is suggested by the extent of present-day aridity have occurred in the relatively recent geological past.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 537–552.     

Phylogenetic diversity of forest trees in the Usambara mountains of Tanzania: correlations with altitude

The relationship between diversity of large trees and altitude was investigated in a Tanzanian tropical rain forest. In total, 231 samples of 20 trees of ≥ 20 cm d.b.h. from the East and West Usambara mountains, covering an elevation range from 280 m to 2180 m a.s.l., were analysed. An ordination demonstrated a constant turnover of species, genera, family and orders with elevation. There were no obvious zones or discontinuities. There was no decline in plot richness with respect to altitude for species, genera or orders. Family richness was shown to increase with altitude. A measure of genetic diversity, the avalanche index, was calculated for each plot to investigate the effect of incorporating phylogenetic relatedness of individuals into the diversity measure. Distances between taxa were extracted from a recent molecular phylogeny of the angiosperms. Incorporation of phylogenetic diversity at family level enhanced the positive correlation between plot diversity and altitude.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 149 , 217–228.     

Phylogeography of the land snail Albinaria hippolyti (Pulmonata: Clausiliidae) from Crete, inferred from ITS-1 sequences

The polytypic Cretan land snail Albinaria hippolyti has a range that is partly fragmented and partly subdivided by hybrid zones. For this reason, it has served as a model species for investigating speciation and radiation in Mediterranean Clausiliidae. The first internal transcribed spacer ( ITS-1 ) of the nuclear ribosomal DNA was sequenced in 20 populations of A. hippolyti and phylogenetically analysed using maximum parsimony. We employed a novel method involving logarithmic weighting of gaps and topological constraints based on bootstrap values. The resulting phylogeography suggests that the species has undergone a recent cycle of range expansion and range reduction. Speciation cannot be linked to major geological vicariance events in the Miocene and Pliocene, as has been suggested previously. The subspecies A. h. arthuriana appears unrelated to other A. hippolyti subspecies, which supports recent suggestions, based on morphology, to regard it as a separate species.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 317–326.     

Uniformity of karyotypes in Ligularia (Asteraceae: Senecioneae), a highly diversified genus of the eastern Qinghai–Tibet Plateau highlands and adjacent areas

Ligularia , a highly diversified genus in the eastern Qinghai–Tibet Plateau and adjacent areas, was chosen as a suitable subject in which to study speciation patterns in this 'hot spot' area at the chromosomal level. Chromosome numbers and karyotypes were studied in 23 populations of 14 species, most of which are endemic to this area. The basic number x  = 29 was confirmed for all species. Ligularia virgaurea was found to have diploid and triploid cytotypes, 2 n  = 58 and 87. Other species are only diploid, with 2 n  = 58. The karyotypes of all populations within any species, and all species spanning most sections and covering most of the morphological range in Ligularia , are very similar to each other, belonging to type 2A according to Stebbin's classification. This karyotype was also found in its close allies, e.g. Cremanthodium , Ligulariopsis , Parasenecio , and Sinacalia . Aneuploid reduction of chromosome number from 2 n  = 60 to 58 and karyotypic variation was found in Ligularia and its allies. Such a chromosomal pattern with few polyploids infers that variation of karyotype structure at the diploid level seems to be the predominant feature of chromosomal evolution in this group and sympatric speciation via hybridization and polyploidization has played a minor role in its species diversity.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 329–342.     

Geometric morphometrics, neural networks and diagnosis of sibling Taterillus species (Rodentia, Gerbillinae)

The lack of diagnostic traits in sibling species means that great quantities of biogeographical and ecological data held in museum collections cannot be utilized effectively, leading to underestimates of biodiversity. In this study we applied neural networks (NN) and canonical variates analyses (CVA) to landmark measurements on the skulls of the West African species Taterillus arenarius , T. petteri , T. gracilis and T. pygargus in an attempt to discriminate species previously identified unambiguously from their karyotypes. Among suggested differences, the relationship between inflation of the tympanic bullae and lower population density is discussed. Cross-validated classification rates did not exceed 73%. Two hypotheses are proposed to explain such high phenotypic similarity: morphological plasticity limited by environmental constraints and the possibility that speciation has been too recent to allow significant morphological divergence.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 319−327.     

The diversity of hemi-epiphytic figs (Ficus ; Moraceae) in a Bornean lowland rain forest

The diversity and niche specificity of hemi-epiphytic figs in a lowland dipterocarp forest in Sarawak were investigated in 1998. Twenty-seven fig species (264 individuals, c. 120 ha) colonized a diversity of host taxa (35 families), but densities were very low and only 1.77% of trees> 30 cm d.b.h. were occupied. There were no significant associations with host taxa or host-bark roughness but among 11 common species (≥9 individuals) the distributions of all other parameters (host-d.b.h., height and position of colonization, crown illumination, soil-texture and slope-angle) were significantly different, and we identified five fig guilds. The guilds corresponded to canopy strata, and appeared to reflect the establishment microsite requirements of different species. A fundamental trade-off within the hemi-epiphytic habit was revealed: Species colonizing larger hosts were rarer, because of lower host densities and more specific microsite requirements, but had better light environments and attained a larger maximum size. The single strangler species appeared to escape many of these constraints, and an important source of mortality caused by host-toppling, indicating the advantages of this strategy. Thus, the hemi-epiphytic figs in this community have come to fill a remarkable diversity of niches, despite low levels of competition, through the exigencies of a complex environment.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78 , 439–455     

Phylogeny and life-history evolution in Carabus (subtribe Carabina: Coleoptera, Carabidae) based on sequences of two nuclear genes

We reconstructed the phylogeny of the holarctic carabid subtribe Carabina (= Carabus s . l. ; Coleoptera, family Carabidae, supertribe Carabitae, tribe Carabini) using sequence data from two nuclear DNA loci: wingless ( Wg ) and phosphoenolpyruvate carboxykinase ( PepCK ). The analysis of the combined data resulted in a well-resolved tree, although Wg and PepCK had partially conflicting phylogenetic signals. The tree topology did not support the reciprocal monophyly of some previously proposed major divisions, whereas all but one of eight other previously proposed subdivisions were recovered as monophyletic clades; the exception was paraphyletic. When two key life-history traits, seasonal life cycle and larval diet, were mapped onto the combined tree, spring breeding (with no larval overwintering) and insectivorous were ancestral traits. Malacophagy has apparently evolved at least twice: once in a small basal group (ten species) and again in a large derived group ( c . 340 species) that accounts for 42% of the species of Carabina. A third type of larva, earthworm feeders, appeared in two related, derived clades and represented moderate species diversity (12%). From the ancestral spring-breeder type with no larval overwintering, autumn-breeder types with larval overwintering apparently evolved repeatedly in insectivorous and malacophagous species, but not in earthworm feeders. Therefore, the extant diversity of the Carabina depends on the high rate of differentiation in the most derived group of malacophagous species.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 135–149.     

Origins, establishment and evolution of new polyploid species: Senecio cambrensis and S. eboracensis in the British Isles

Two new polyploid species of Senecio have originated in the British Isles in recent times following hybridization between native S. vulgaris (2 n  = 40) and introduced S. squalidus (2 n  = 20). One of these is the allohexaploid S. cambrensis (2 n  = 60), the other is the recombinant tetraploid S. eboracensis (2 n  = 40). We review what is known about when and how each species originated, and their reproductive isolation from parents due to high selfing rates. We also review evidence that suggests S. cambrensis may have undergone rapid genome evolution since its origin, and comment on the risks of extinction to each species due to chance factors operating during the early establishment phase. The discovery of both species soon after their origin provides an unparalleled opportunity to examine two different but related forms of speciation following hybridization between the same parent species. Further detailed study of the ecology and genomics of S. cambrensis and S. eboracensis will help improve our understanding of the process of polyploid speciation in plants.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 467–474.     

Rapid radiation of the Mediterranean Luciobarbus species (Cyprinidae) after the Messinian salinity crisis of the Mediterranean Sea, inferred from mitochondrial phylogenetic analysis

Phylogenetic relationships of 64 freshwater Barbus s.s. species distributed in basins around the Mediterranean Sea were assessed using cytochrome b sequences. Our results are in concordance with previous morphological and genetic studies, which proposed that these species belong to two major lineages (or subgenera): Barbus and Luciobarbus . We were particularly interested in phylogenetic relationships among species of the Luciobarbus lineage that are primarily found in the southern Mediterranean region from the Iberian Peninsula to the Middle East. In the Luciobarbus lineage, species that were previously attributed to the Capoeta genus were clustered. In this study, we observed short internodes between monophyletic groups having a geographical agreement around the Mediterranean. However, groups from the opposite sides of the Mediterranean Sea (Iberian Peninsula– Capoeta , north-western Africa–Middle East) seem to be phylogenetically close. We therefore infer that rapid radiation of Luciobarbus species in the Late Miocene better fits our data rather than gradual founder events in the southern Mediterranean. We propose that the biogeographical event along an east–west route, responsible for the present distribution of Luciobarbus species, was the 'Lago Mare' phase of the Mediterranean Sea that provided a rapid dispersal route over extensive distances. This provides new insights into the speciation pattern of this group, and may be of general use in the study of freshwater species in these regions.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 207–222.     

New chromosome counts in the Centaurea Jacea group (Asteraceae, Cardueae) and some related taxa

Twenty-seven chromosome counts are reported in 23 species of the genus Centaurea , mostly eastern endemic species of the Jacea group, which has become the core of the re-defined genus Centaurea . Twenty reports are new, one is a correction of a previous count, one is a confirmation of limited previous data and one represents a new basic number in the Centaureinae. The prevalence of the basic chromosome number x  = 9 among the Eastern sections of the Jacea group is confirmed, together with the close correlation between karyological data and classification of the genus. Two alternative hypotheses on the aberrant chromosome number (for the Centaureinae) found in C. behen are proposed. One of them, if verified, would confirm that a cycle of polyploidy and descending dysploidy is a key mechanism in the speciation of the group.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 345–352.     

Markedly discordant mitochondrial DNA and allozyme phylogenies of tube-nosed fruit bats, Nyctimene, at the Australian–Oriental biogeographical interface

Australo-Papuan tube-nosed fruit bats of the genus Nyctimene reach their most westerly distribution on the island archipelagos of eastern Indonesia. A recent morphological examination indicates three species occur on Moluccan islands. Both allozyme electrophoresis and mitochondrial DNA (mtDNA) sequencing reveal there are only two species present, Nyctimene cephalotes and Nyctimene albiventer , but there is considerable disparity between the results obtained from the two genetic data sets. Allozyme data indicate N. albiventer occurs on Wokam, which sits on the Australian continental shelf and was joined to Australo-Papua during the last glacial maximum, and N. cephalotes on the other Moluccan islands, all of which are off the continental shelf. Divergence of these two species is dated at approximately 1.5 Mya. By contrast, the mtDNA gene tree shows two deep clades, one containing all specimens from Wokam and Yamdena, and the second all the specimens from the other islands. This especially marked incongruence between the two genetic data sets is ascribed to either a single introgression event of N. albiventer mtDNA into N. cephalotes on Yamdena at around 100 000 ya or lineage sorting of very old mtDNA lineages that coalesce a rather long time before the speciation event. These results highlight that caution should be exercised when relying on mtDNA as barcodes in species taxonomy. The continental-associated N. albiventer on Wokam has higher levels of allozyme heterozygosity and mtDNA nucleotide diversity than the N. cephalotes populations occurring on the more remote islands, indicating that this colonizing species has experienced bottlenecks and/or a low effective population size since speciation.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 589–602.     

Species richness and structure of three Neotropical bat assemblages

We compared the assemblages of phyllostomid bats in three Neotropical rainforests with respect to species richness and assemblage structure and suggested a method to validate estimates of species richness for Neotropical bat assemblages based on mist-netting data. The fully inventoried bat assemblage at La Selva Biological Station (LS, 100 m elevation) in Costa Rica was used as a reference site to evaluate seven estimators of species richness. The Jackknife 2 method agreed best with the known bat species richness and thus was used to extrapolate species richness for an Amazonian bat assemblage (Tiputini Biodiversity Station; TBS, 200 m elevation) and an Andean premontane bat assemblage (Podocarpus National Park; BOM, 1000 m elevation) in Ecuador. Our results suggest that more than 100 bat species occur sympatrically at TBS and about 50 bat species coexist at BOM. TBS harbours one of the most species-rich bat assemblages known, including a highly diverse phyllostomid assemblage. Furthermore, we related assemblage structure to large-scale geographical patterns in floral diversity obtained from botanical literature. Assemblage structure of these three phyllostomid assemblages was influenced by differences in floral diversity at the three sites. At the Andean site, where understorey shrubs and epiphytes exhibit the highest diversity, the phyllostomid assemblage is mainly composed of understorey frugivores and nectarivorous species. By contrast, canopy frugivores are most abundant at the Amazonian site, coinciding with the high abundance of canopy fruiting trees. Assemblage patterns of other taxonomic groups also may reflect the geographical distribution patterns of floral elements in the Andean and Amazonian regions.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 617–629.     

Molecular phylogeny and zoogeography of the freshwater crayfish genus Cherax Erichson (Decapoda: Parastacidae) in Australia

The evolutionary history and biogeography of freshwater-dependent taxa in Australia is of intrinsic interest given the present-day aridity of this continent. Cherax is the most widespread and one of the most species-rich of Australia's nine freshwater crayfish genera. The phylogenetic relationships amongst 19 of the 23 Australian Cherax were established from mitochondrial DNA sequences representing the 12S rRNA and 16S rRNA gene regions. The relationships among species support an initial east–west separation, followed by a north–south divergence in eastern Australia. Molecular clock estimations suggest that these divergences date back to the Miocene. The phylogenetic relationships support endemic speciation within geographical regions and indicate that long-distance dispersal has not led to recent speciation as previously hypothesized. This new evolutionary scenario is consistent with the climatic history of Australia and the evolutionary history of other similarly distributed freshwater-dependent organisms in Australia.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 553–563.     

Patterns of diversification on old volcanic islands as revealed by the woodlouse-hunter spider genus Dysdera (Araneae, Dysderidae) in the eastern Canary Islands

Long-term erosion and subsidence cause dramatic alterations in the physical and ecological features of oceanic islands. Although oceanic islands have been extensively used as models for the study of speciation, little attention has been given to investigating evolutionary patterns in old volcanic islands that have suffered severe climatic degradation. The spider genus Dysdera has diversified across the Canary Islands and has evolved endemisms in the low-elevation, xeric eastern islands, which sharply contrast with the younger, higher, and more humid western islands. A combined phylogenetic analysis of seven mitochondrial and nuclear genes reveals that the eastern Canaries were colonized twice, although only one lineage underwent in situ diversification. Origins of the speciose lineage remain obscure, but probably preceded diversification of present-day Iberian and North African species. A second colonization of the eastern Canaries from North Africa has occurred in more recent times. Molecular analyses reveal several instances of geographically coherent cryptic lineages further supported by morphometric evidence. Analyses of diversification rates suggest deceleration of diversification over the course of time, and this is compatible with increasing extinction rates due to drastic yet continuous ecological changes. Extinction may also explain incongruent patterns of morphological differentiation and species coexistence. Despite a general trend towards community impoverishment, there is also evidence for recent speciation events linked to ecological shifts, which may illustrate the origins of nonspeciose relic lineages on islands.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 589–615.     

Molecular diversification of salamanders of the tropical American genus Bolitoglossa (Caudata: Plethodontidae) and its evolutionary and biogeographical implications

The largest genus of salamanders, Bolitoglossa (Plethodontidae), is widespread in tropical America, where it occurs in diverse habitats and elevations, from high elevation grasslands to lowland rain forest . It has the most extensive geographical range of any salamander genus. While most species occur in Middle America, it ranges throughout most of tropical South America as well. Phylogenetic analysis of 1196 bp of two mitochondrial genes (cytochrome b , 16S RNA) from 55 species offers strong support for the monophyly of the genus and sorts the species into a number of clades. Taking into account morphology, distribution, general ecology, and prior systematic and taxonomic studies, we recognize seven subgenera, four of them new: Bolitoglossa Duméril, Bibron et Duméril, 1854, Eladinea Miranda Ribeiro, 1937, Magnadigita Taylor, 1944, Mayamandra , Nanotriton , Oaxakia and Pachymandra . All South American and some lower Middle American species are included in a single well -supported clade, Eladinea . At the species level our analyses uncover the existence of large genetic diversity within morphologically homogeneous taxa. We propose the new combination: B. (Eladinea) paraensis (Unterstein, 1930) stat. nov. , for Brazilian salamanders previously included under B. altamazonica . We evaluate evidence for the multiple colonization of the tropical lowlands by morphologically derived species groups. South America was invaded by members of one clade, Eladinea , which we infer to have dispersed to South America prior to closure of the Panamanian Portal. Despite the relatively long history of salamanders in South America, that continent now accounts for a relatively small proportion of the lineages and species of neotropical salamanders.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81 , 325–346.     

Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event

The Australian populations of the green-eyed tree frog Litoria genimaculata consist of a northern and southern genetic lineage that meet in a mosaic contact zone comprising two independent areas of contact: one where the main ranges of the lineages overlap, and the second where a population of the southern lineage is isolated within the range of the northern lineage. A recent study failed to find significant reproductive isolation between the main ranges of the two lineages, despite deep genetic divergence, partial postzygotic isolation, and call differences. The study did, however, demonstrate rapid phenotypic divergence and speciation of the isolated population of the southern lineage from both the parapatric northern lineage and from the allopatric, but genetically similar, main range of the southern lineage. Herein, the isolated population of the southern lineage is described as a distinct species, Litoria myola sp. nov. , whereas the remainder of the southern lineage and the northern lineage are retained as a single, paraphyletic species, Litoria genimaculata . Resolving this unusual systematic situation demonstrates the value of using multiple lines of evidence in delimiting species. Litoria myola sp. nov. has a very small distribution and population size and warrants a Critically Endangered listing (B1, 2) under IUCN criteria. Threats and management recommendations are outlined, and the conservation of hybrid zones as areas of evolutionary novelty is discussed.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 549–563.     

Molecular phylogeny of wood mice (Apodemus, Muridae) in East Asia

Sequences of the mitochondrial cytochrome b (1140 bp) and nuclear IRBP (1152 bp) genes were used to assess the evolutionary history of Apodemus , using the complete set of Asian species. Our results indicate that speciation in Asia involved three radiations, which supports an earlier study. The initial radiation yielded A. argenteus (Japanese endemic), A. gurkha (Nepalese endemic), and the ancestral lineage of the remaining Asian species. This lineage subsequently diverged into four groups: agrarius-chevrieri ( agrarius group), draco-latronum-semotus ( draco group), A. peninsulae , and A. speciosus (Japanese endemic). The final step consisted of divergence within two species groups as a consequence of the geography of the Yunnan-Guizhou plateau and Taiwan. The ecological ability of two Apodemus species to inhabit one locality via niche partitioning likely drove the second radiation and shaped the basic geographical pattern seen today: A. argenteus and A. speciosus in Japan, A. agrarius and A. peninsulae in northern China, and the A. agrarius and A. draco groups in southern China. The three radiations are estimated to have occurred 7.5, 6.6, and 1.8–0.8 Mya respectively, using the IRBP clock, based on rat–mouse divergence 12 Mya.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 469–481.     

A new species of Ceratozamia (Zamiaceae) from Tabasco and Chiapas, Mexico

Ceratozamia becerrae sp. nov. is described and illustrated. This species from Tabasco and Chiapas has affinity with C. miqueliana H. Wendl. from Veracruz and Chiapas, but differs in morphology and habit of leaves, leaflets, male and female strobili and trunk. Ceratozamia becerrae is considered part of the C. miqueliana species complex that includes C. miqueliana, C. euryphyllidia Vázq.Torres, Sabato & Stevenson and C. zoquorum Pérez-Farrera, Vovides & Iglesias. The geographical range of this species complex is southern Veracruz, Tabasco and northern Chiapas in tropical rain forests.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 123–128.