Phylogeography of the lacertid lizard, Psammodromus algirus, in Iberia and across the Strait of Gibraltar

Aim  To determine genetic substructuring within the lacertid lizard Psammodromus algirus . To compare levels of variation across a geological barrier, the Strait of Gibraltar, and to compare this against the known age of the barrier using a molecular clock hypothesis. To compare the effect of the barrier within this species with previously published data from other organisms.
Location  The Iberian Peninsula and North Africa.
Methods  Partial sequences from the mitochondrial cytochrome b , 12S rRNA and 16S rRNA genes were obtained from 101 specimens belonging to the subfamily Gallotiinae and used in this study. The data set was aligned using C lustal X and phylogenetic trees produced using both maximum-parsimony and maximum-likelihood methods. Maximum likelihood estimates of divergence times for the combined data set (12S + 16S + cytochrome b ) were obtained after discovery of lineage rate constancy across the tree using a likelihood ratio test.
Results  Psammodromus algirus contains divergent eastern and western mtDNA clades within the Iberian Peninsula. The western clade has northern and southern lineages in Iberia and one in North Africa. This phylogeographical pattern indicates that the lizard invaded North Africa after the opening of the Strait, presumably by natural rafting.
Main conclusions  As in several other species, current patterns of genetic diversity within P. algirus are not directly related to the opening of the Strait of Gibraltar. Widespread sampling on both sides of the barrier is necessary to determine its effect on species in this area accurately.     

Molecular phylogeny of the antitropical subgenus Goniistius (Perciformes: Cheilodactylidae: Cheilodactylus): evidence for multiple transequatorial divergences and non-monophyly

The subgenus Goniistius comprises eight species of marine nearshore fishes which are antitropically distributed. The molecular phylogeny of these and other cheilodactylids was reconstructed from cytochrome oxidase I and cytochrome b mitochondrial DNA sequences. The placement within Goniistius of the morphologically divergent species Cheilodactylus (G.) nigripes was not supported. The remaining seven species are sufficiently divergent from other cheilodactylids to be designated as a separate genus. The antitropical distribution oi Goniistius is the result of three transequatorial divergences, which occurred during two periods. Based on molecular clock calibrations, these periods are suggested to be the mid Miocene, and late Miocene to early Pliocene. It is not known in which direction or by which mechanism these transequatorial divergences occurred, although biogeographic hypotheses of Mesozoic or Pleistocene separations can be discounted. The degree of genetic divergence between North and South Pacific populations of C. (G.) mttatus Garrett indicates that they have undergone cryptic speciation.     

Long-distance gene flow and cross-Andean dispersal of lowland rainforest bees (Apidae: Euglossini) revealed by comparative mitochondrial DNA phylogeography

Euglossine bees (Apidae; Euglossini) exclusively pollinate hundreds of orchid species and comprise up to 25% of bee species richness in neotropical rainforests. As one of the first studies of comparative phylogeography in a neotropical insect group, we performed a mitochondrial DNA (mtDNA)-based analysis of 14 euglossine species represented by populations sampled across the Andes and/or across the Amazon basin. The mtDNA divergences within species were consistently low; across the 12 monophyletic species the mean intraspecific divergence among haplotypes was 0.9% (range of means, 0-1.9%). The cytochrome oxidase 1 (CO1) divergence among populations separated by the Andes (N = 11 species) averaged 1.1% (range 0.0-2.0%). The mtDNA CO1 data set displayed homogeneous rates of nucleotide substitution, permitting us to infer dispersal across the cordillera long after the final Andean uplift based on arthropod molecular clocks of 1.2-1.5% divergence per million years. Gene flow across the 3000-km breadth of the Amazon basin was inferred from identical cross-Amazon haplotypes found in five species. Although mtDNA haplotypes for 12 of the 14 euglossine species were monophyletic, a reticulate CO1 phylogeny was recovered in Euglossa cognata and E. mixta, suggesting large ancestral populations and recent speciation. Reference to closely related outgroups suggested recent speciation for the majority of species. Phylogeographical structure across a broad spatial scale is weaker in euglossine bees than in any neotropical group previously examined, and may derive from a combination of Quaternary speciation, population expansion and/or long-distance gene flow.     

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.     

Historical transoceanic dispersal of a freshwater shrimp: the colonization of the South Pacific by the genus Paratya (Atyidae)

Aim To infer the phylogenetic relationships within the freshwater shrimp genus Paratya Miers, 1882 (Atyidae) and to use these data to answer biogeographical questions about the location, timing and form of evolution of this genus in the South Pacific. Location Paratya are spread throughout various freshwater habitats in the western Pacific, with a disjunct northern range in the North Pacific (Japan, Korea, Ryukyu Islands, Siberia) and South Pacific (Australia, New Zealand, New Caledonia, Lord Howe, Norfolk Island). Methods Specimens were obtained from throughout its range. Mitochondrial sequences of cytochrome oxidase subunit I and 16S ribosomal DNA were analysed using phylogenetic techniques to identify whether landmasses are monophyletic and what the relationships are between landmasses. Molecular clock dating methods were used to date divergences between taxa. Results Each landmass was recovered as monophyletic. Japan/Ryukyu Islands is the most basal group, followed by New Zealand. Australian specimens form a sister group to a clade made up of two groups (New Caledonia and Lord Howe/Norfolk Island). The oldest divergence within the genus (between North and South Pacific) took place 12–19 Ma. Main conclusions The geographical origin of the genus (either Gondwana or Laurasia) is unclear. Dispersal occurred between the North and South Pacific long after the split up of Gondwana. Dispersal likely explains the presence of Paratya on each landmass in the South Pacific, from continent to isolated oceanic island. This dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya, given that amphyidromy is plesiomorphic in atyid shrimp.     

Molecular systematics of the Chrysoperla carnea group (Neuroptera: Chrysopidae) in Europe

The green lacewing Chrysoperla carnea is a complex of cryptic species whose differentiation has been so far based upon morphology, ecophysiology, behaviour and preliminary mitochondrial DNA data using cytochrome oxidase subunit II (COII) and NADH dehydrogenase subunit II. In this work we extended the DNA data by screening nucleotide sequences of COII, cytochrome oxidase I, cytochrome b and the large ribosomal subunit of the mtDNA. These new data suggest that C. carnea s.s. is a well-supported, separate taxon, but that other taxa of the complex are not consistently differentiated by the current DNA data.     

Molecular phylogeny of the genus Mus (Rodentia: Murinae) based on mitochondrial and nuclear data

The genus Mus encompasses at least 38 species divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . The subgenus Mus , which comprises the house mouse and related species, is by far the most extensively studied, although the subgenus Nannomys is the most speciose. Although the relationships within the subgenus Mus are rather well characterized, those between subgenera are still unclear. In the present study, phylogenetic analyses of the whole genus were performed using a larger species sample of Nannomys than in previous studies, and a nuclear gene (IRBP) in addition to mitochondrial data (cytochrome b and 12S rRNA). Members of the Acomyinae and Murinae were used as outgroups. Separate and combined analyses were performed with maximum parsimony, maximum likelihood and Bayesian methods, and divergence times were estimated. The results showed that the monophyly of the genus Mus and of each subgenus was strongly supported by the three genes and the combined analysis. The phylogenies derived from the three genes were on the whole congruent; however, several conflicting topologies were observed such as the relationships between the three Asian species of the subgenus Mus ( caroli , cervicolor and cookii ). Increasing the taxonomic sampling of Nannomys did not satisfactorily improve the resolution of relationships between the four subgenera. In addition, molecular calibrations indicate that the Mus and Nannomys radiation coincided with major environmental changes.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 417–427.     

Microsatellite DNA and behavioural studies provide evidence of host-mediated speciation in Myzus persicae (Hemiptera: Aphididae)

The fossil record of mammals records a major interchange of northern and southern faunas in the New World, upon closure of the Panamanian isthmus approximately 3 Mya, termed the Great American Biotic Interchange (GABI). Due to their poor preservation in the fossil record, the degree of participation of birds in this interchange remains largely unknown. A phylogeny for wrens of the genus Campylorhynchus (Aves: Passeriformes) was reconstructed using DNA sequences from the mitochondrial control region and cytochrome b gene. This phylogeny, in combination with biogeographical inference and molecular clock methods, allows estimates of the importance of Late Pliocene interchange to the history of the group. Biogeographical reconstructions and divergence date estimates suggest that the genus began diversification in North America prior to closure of the Panamanian isthmus, consistent with a hypothesized North American origin for the family Troglodytidae. These reconstructions are consistent with pre-GABI dispersal of at most a single Campylorhynchus lineage into South America, with subsequent dispersal of additional lineages, probably across the fully formed isthmus. Increased sampling of avian taxa with widespread New World distributions will continue to clarify the timing and direction of continental interchange.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 687–702.     

Genomic variation in the mitochondrially encoded cytochrome b (MT-CYB) and 16S rRNA (MT-RNR2) genes: characterization of eight endangered Pecoran species

In an effort to develop species-specific identification markers, we examined genetic variants and molecular signatures within genes encoding mitochondrial cytochrome b and 16S rRNA in eight endangered Pecoran species endemic to the Indian peninsula. Our results revealed that the cytochrome b gene exhibited higher sequence diversity than the 16S rRNA gene, both between and within species. However, the 16S rRNA gene harboured a larger number of species-specific mutation sites compared with the cytochrome b gene, suggesting that it could be useful for species identification. Indeed, we successfully used 'forensically informative nucleotide sequencing' (FINS) analysis of the 16S rRNA gene to identify two previously unknown biological specimens.     

Time and space in biogeography: response to Parenti & Ebach (2013)

A recent Guest Editorial by Parenti & Ebach (2013, Journal of Biogeography, 40, 813–820) disagrees with the methods or interpretations in two of our recent papers. In addition, the authors open a debate on biogeographical concepts, and present an alternative philosophy for biogeographical research in the context of their recently described biogeographical subregion called ‘Pandora’. We disagree with their approach and conclusions, and comment on several issues related to our differing conceptual approaches for biogeographical research; namely, our use of molecular phylogenetic analyses, including time estimates; and Parenti & Ebach's reliance on taxon/general area cladograms. Finally, we re‐examine their ‘tests’ supporting the existence of ‘Pandora’.     

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.     

The Hawaiian Archipelago is a stepping stone for dispersal in the Pacific: an example from the plant genus Melicope (Rutaceae)

Aim Pacific biogeographical patterns in the widespread plant genus Melicope J.R. Forst. & G. Forst. (Rutaceae) were examined by generating phylogenetic hypotheses based on chloroplast and nuclear ribosomal sequence data. The aims of the study were to identify the number of colonization events of Melicope to the Hawaiian Islands and to reveal the relationship of Hawaiian Melicope to the Hawaiian endemic genus Platydesma H. Mann. The ultimate goal was to determine if the Hawaiian Islands served as a source area for the colonization of Polynesia. Location Nineteen accessions were sampled in this study, namely eight Melicope species from the Hawaiian Islands, four from the Marquesas Islands, one species each from Tahiti, Australia and Lord Howe Island, two Australian outgroups and two species of the Hawaiian endemic genus Platydesma. To place our results in a broader context, 19 sequences obtained from GenBank were included in an additional analysis, including samples from Australia, Papua New Guinea, New Zealand, Southeast Polynesia and Asia. Methods DNA sequences were generated across 19 accessions for one nuclear ribosomal and three chloroplast gene regions. Maximum parsimony analyses were conducted on separate and combined data sets, and a maximum likelihood analysis was conducted on the combined nuclear ribosomal and chloroplast data set. A broader nuclear ribosomal maximum parsimony analysis using sequences obtained from GenBank was also performed. Geographic areas were mapped onto the combined chloroplast and nuclear ribosomal tree, as well as onto the broader tree, using the parsimony criterion to determine the dispersal patterns. Results Phylogenetic analyses revealed that Platydesma is nested within Melicope and is sister to the Hawaiian members of Melicope. The Hawaiian Melicope + Platydesma lineage was a result of a single colonization event, probably from the Austral region. Finally, Marquesan Melicope descended from at least one, and possibly two, colonization events from the Hawaiian Islands. Main conclusions These data demonstrate a shifting paradigm of Pacific oceanic island biogeography, in which the patterns of long‐distance dispersal and colonization in the Pacific are more dynamic than previously thought, and suggest that the Hawaiian Islands may act as a stepping stone for dispersal throughout the Pacific.     

Ocean barriers and glaciation: evidence for explosive radiation of mitochondrial lineages in the Antarctic sea slug Doris kerguelenensis (Mollusca, Nudibranchia)

Strong currents and deep passages of water can be barriers for larval dispersal of continental marine animals, but potential effects on direct developers are under-investigated. We examined the genetic structure of Doris kerguelenensis , a directly developing sea slug that occurs across the Drake Passage, the body of water separating Antarctica from South America. We found deep mitochondrial divergences within populations on both sides of the Drake Passage, and South American animals formed multiple sister-group relationships with Antarctic animals. A generalised molecular clock suggested these trans-Drake pairs diverged during the Pliocene–Pleistocene, after the formation of the Drake Passage. Statistical parsimony methods recovered 29 separate haplotype networks (many sympatric) that likely correlate with allopatric events caused by repeated glacial cycles. Data from 16S were congruent but more conserved than COI, and the estimated ancestral 16S haplotype was widespread. The marked difference in the substitution rates between these two mitochondrial genes results in different estimates of connectivity. Demographic analyses on networks revealed some evidence for selection and expanding populations. Contrasting with the Northern Hemisphere, glaciation in Antarctica appears to have increased rather than reduced genetic diversity. This suggests orbitally forced range dynamics based on Northern Hemisphere phylogeography do not hold for Antarctica. The diverse lineages found in D. kerguelenensis point towards a recent, explosive radiation, likely reflecting multiple refuges during glaciation events, combined with limited subsequent dispersal. Whether recognised as cryptic species or not, genetic diversity in Antarctic marine invertebrates appears higher than expected from morphological analyses, and supports the Antarctic biodiversity pump phenomenon.     

Open-ocean barriers to dispersal: a test case with the Antarctic Polar Front and the ribbon worm Parborlasia corrugatus (Nemertea: Lineidae)

Open-ocean environments provide few obvious barriers to the dispersal of marine organisms. Major currents and/or environmental gradients potentially impede gene flow. One system hypothesized to form an open-ocean dispersal barrier is the Antarctic Polar Front, an area characterized by marked temperature change, deep water, and the high-flow Antarctic Circumpolar current. Despite these potential isolating factors, several invertebrate species occur in both regions, including the broadcast-spawning nemertean worm Parborlasia corrugatus. To empirically test for the presence of an open-ocean dispersal barrier, we sampled P. corrugatus and other nemerteans from southern South America, Antarctica, and the sub-Antarctic islands. Diversity was assessed by analyzing mitochondrial 16S rRNA and cytochrome c oxidase subunit I sequence data with Bayesian inference and tcs haplotype network analysis. Appropriate neutrality tests were also employed. Although our results indicate a single well-mixed lineage in Antarctica and the sub-Antarctic, no evidence for recent gene flow was detected between this population and South American P. corrugatus. Thus, even though P. corrugatus can disperse over large geographical distances, physical oceanographic barriers (i.e. Antarctic Polar Front and Antarctic Circumpolar Current) between continents have likely restricted dispersal over evolutionary time. Genetic distances and haplotype network analysis between South American and Antarctic/sub-Antarctic P. corrugatus suggest that these two populations are possibly two cryptic species.     

The cyprinodont fish Rivulus (Aplocheiloidei: Rivulidae) in Trinidad and Tobago: molecular evidence for marine dispersal, genetic isolation and local differentiation

Mitochondrial DNA sequences (756 bp) were obtained from the cytochrome b gene of 36 Rivulus individuals collected from 10 sites in Trinidad and one site in Tobago. Eight haplotypes were identified. Low genetic divergence (0.5%) between one western Trinidad (Blue Basin) haplotype and Rivulus hartii from north-western Venezuela (Paria peninsula) and high genetic divergence ( c. 11%) between these and the remaining other Trinidad and Tobago haplotypes suggests that the islands were colonized by two lineages. The commoner haplotype is distributed throughout lowland Trinidad, possibly a reflection of flooding of the Orinoco River leading to high dispersal between watersheds. Rivulus from higher altitude (Northern Range) localities that would not have been affected by such flooding show high genetic divergence between sites. The genetic differentiation between northern and southern watersheds suggests isolation between some of these drainages.     

Phylogeography of the Rhabditis (Pellioditis) marina species complex: evidence for long-distance dispersal, and for range expansions and restricted gene flow in the northeast Atlantic

Pinpointing processes that structure the geographical distribution of genetic diversity of marine species and lead to speciation is challenging because of the lack of obvious dispersal barriers and the likelihood of substantial (passive) dispersal in oceans. In addition, cryptic radiations with sympatric distributions abound in marine species, challenging the allopatric speciation mechanism. Here, we present a phylogeographical study of the marine nematode species complex Rhabditis ( Pellioditis ) marina to investigate processes shaping genetic structure and speciation. Rhabditis ( P .) marina lives on decaying macroalgae in the intertidal, and may therefore disperse over considerable distances. Rhabditis ( P .) marina consists of several cryptic species sympatrically distributed at a local scale. Genetic variation in the COI gene was screened in 1362 specimens from 45 locations around the world. Two nuclear DNA genes (ITS and D2D3) were sequenced to infer phylogenetic species. We found evidence for ten sympatrically distributed cryptic species, seven of which show a strong genetic structuring. A historical signature showed evidence for restricted gene flow with occasional long-distance dispersal and range expansions pre-dating the last glacial maximum. Our data also point to a genetic break around the British Isles and a contact zone in the Southern Bight of the North Sea. We provide evidence for the transoceanic distribution of at least one cryptic species (PmIII) and discuss the dispersal capacity of marine nematodes. The allopatric distribution of some intraspecific phylogroups and of closely related cryptic species points to the potential for allopatric speciation in R. ( P .) marina .     

Phylogeny and adaptive radiation in the Onychopoda (Crustacea,Cladocera): evidence from multiple gene sequences

Members of the order Cladocera show remarkable morphological and ecological diversity. One of the most spectacular adaptive radiations in this group has involved species of the suborder Onychopoda, which have adopted a novel feeding strategy, predation, and have colonized habitats with a broad range of salinities. In order to evaluate the origins and systematics of this group, we derived a molecular phylogeny for its three component families including nine of 10 recognized genera based on three mitochondrial (mt) gene sequences: cytochrome c oxidase subunit I (COI), the ribosomal small and large subunits (12S and 16S) and one nuclear gene sequence: the small ribosomal subunit (18S). Maximum‐parsimony, maximum‐likelihood and neighbour‐joining phylogenetic analyses were largely congruent, supporting the monophyly of the suborder and each of its families. Comparative analyses of data based on total evidence and the conditional combination of the ribosomal genes produced relatively congruent patterns of phylogenetic affinity. By contrast, analyses of single gene results were inconsistent in recovering the monophyletic groups identified by the multigene analyses. Based on the reconstructed phylogeny, we discriminate among the existing hypotheses regarding the evolutionary history of the onychopods. We identify a prolonged episode of speciation from the Miocene to the Pleistocene with two pulses of diversification. We discuss our results with reference to the geological history of the Ponto‐Caspian basin, the region which fostered the onychopod radiation.     

Molecular and morphological data reveal cryptic taxonomic diversity in the terrestrial slug complex Arion subfuscus/fuscus (Mollusca, Pulmonata, Arionidae) in continental north-west Europe

The importance and abundance of cryptic species among invertebrate taxa is well documented. Nowadays, taxonomic, phylogenetic and conservation biological studies frequently use molecular markers to delineate cryptic taxa. Such studies, however, often face the problem of the differential resolution of the molecular markers and techniques involved. This issue is explored in the present study of cryptic taxa within the terrestrial slug complex Arion subfuscus/fuscus in continental north-west Europe. To this end, morphological, allozyme and mitochondrial 16S rDNA sequence data have been jointly evaluated. Using allozyme data and gonad type, two distinct groups were consistently delineated, even under sympatric conditions. The 16S rDNA data strongly supported both those groups and even suggested the presence of three distinct taxa within one of them. However, in view of: (1) the allopatric distribution of three OTUs, (2) the lack of allozyme or morphological differentiation, and (3) the extremely high degree of intraspecific mtDNA variation reported in pulmonate gastropods, they are, for the time being, not regarded as valid species under the biological species concept. By means of 16S rDNA and allozyme data, the position of type and topotype material of A. subfuscus s.s. and A. fuscus relative to the newly defined OTUs was determined, thus clarifying the nomenclature of this species complex. Additionally, gonad type proved to be a useful character for distinguishing the two species in north-west Europe.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 23–38.