Comparative Phylogeography of the Atlantic Forest Endemic Sloth (Bradypus torquatus) and the Widespread Three-toed Sloth (Bradypus variegatus) (Bradypodidae, Xenarthra)

The comparative phylogeographic study of the maned sloth (Bradypus torquatus) and the three-toed sloth (Bradypus variegatus) was performed using a segment of mitochondrial DNA (mtDNA) control region. We examined 19 B. torquatus from two regions and 47 B. variegatus from three distant regions of Atlantic forest. This first characterization of molecular diversity indicates a great diversity (B. torquatus: h = 0.901 ± 0.039 and π = 0.012 ± 0.007; B. variegatus: h = 0.699 ± 0.039 and π = 0.010 ± 0.006) and very divergent mitochondrial lineages within each sloth species. The different sampled regions carry distinct and non-overlapping sets of mtDNA haplotypes and are genetically divergent. This phylogeographic pattern may be characteristic of sloth species. In addition, we infer that two main phylogeographic groups exist in the Atlantic forest representing a north and south distinct divergence.     

The Influence of Pleistocene Climatic Changes and Ocean Currents on the Phylogeography of the Southern African Barnacle,Tetraclita serrata (Thoracica; Cirripedia)

The evolutionary effects of glacial periods are poorly understood for Southern Hemisphere marine intertidal species, particularly obligatory sessile organisms. We examined this by assessing the phylogeographic patterns of the southern African volcano barnacle, Tetraclita serrata, a dominant species on rocky intertidal shores. Restricted gene flow in some geographical areas was hypothesized based on oceanic circulation patterns and known biogeographic regions. Barnacle population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (COI) region for 410 individuals sampled from 20 localities spanning the South African coast. The mtDNA data were augmented by generating nuclear internal transcribed spacer 1 (ITS1) sequences from a subset of samples. Phylogenetic and population genetic analyses of mitochondrial DNA data reveal two distinct clades with mostly sympatric distributions, whereas nuclear analyses reveal only a single lineage. Shallow, but significant structure (0.0041–0.0065, P<0.01) was detected for the mtDNA data set, with the south-west African region identified as harbouring the highest levels of genetic diversity. Gene flow analyses on the mtDNA data show that individuals sampled in south-western localities experience gene flow primarily in the direction of the Benguela Current, while south and eastern localities experience bi-directional gene flow, suggesting an influence of both the inshore currents and the offshore Agulhas Current in the larval distribution of T. serrata. The mtDNA haplotype network, Bayesian Skyline Plots, mismatch distributions and time since expansion indicate that T. serrata population numbers were not severely affected by the Last Glacial Maximum (LGM), unlike other southern African marine species. The processes resulting in the two morphologically cryptic mtDNA lineages may be the result of a recent historical allopatric event followed by secondary contact or could reflect selective pressures due to differing environmental conditions.     

Marine fishes (Elasmobranchii and Teleostei) from the Santana Archipelago,a Marine Protected Area in the southwestern Atlantic

The Santana Archipelago (22°23′S, 41°42′W) is located at the northern limit of the South Brazil Bight in Southeastern Brazil, a major topographic feature of the South American continental shelf relevant in terms of fisheries, biogeography and conservation. Herein, the first inventory of the ichthyofauna of the Santana Archipelago is presented, with information on the distribution and conservation status of 147 species of the Teleostei and Elasmobranchii. Sampling was performed during 15 field expeditions between March 2013 and November 2015. A total of 6931 specimens were collected using bottom trawl, beach seine, hand net and scuba diving. Records of 28 species were based on photographs, and five species were recorded through underwater sighting. The Elasmobranchii was represented by nine species in eight families and six orders, and the Teleostei by 138 species in 54 families and 26 orders. Previous records of fishes from the Archipelago consist of 18 species deposited in fish collections; therefore, 129 species are reported herein for the first time. Most (114, 77.5%) species have large geographic distributions (western Atlantic: 81 species, 55.1%; eastern and western Atlantic: 33 species, 22.4%), but seven recorded species (4.8%) are endemic to the Brazilian Province. At the Global (IUCN) level, 12 species (8.1%) are threatened with extinction. Thirteen (8.8%) species are also considered as threatened at the Regional (Brazilian) level. These results highlight the relevance of the Santana Archipelago in the Brazilian conservationist context. Possible threats to the ichtyofauna of the Archipelago are discussed, and effective measures of conservation are presented.     

Random Amplified Polymorphic DNA (RAPD) Variation among Populations of the Insular Endemic Plant Campanula microdonta(Campanulaceae)

RAPD variation was examined in nine populations of Campanulamicrodonta Koidz., endemic to the Izu Islands, Japan. Ninety-eightbands were obtained for all populations, 94% of which were polymorphicat least within a population. Shannon's H values were calculated;these have frequently been used in RAPD studies to estimategenetic diversity. The values within populations did not correlatewith the allozyme gene diversity estimated by a previous studyor with distance from the Japanese mainland. The possible reasonsfor this discrepancy are different selection regimes betweenthe two markers, higher RAPD mutation rates, and each marker'sdifferent coverage of genomes. Cluster analysis of genetic similaritiessuggested that colonization of each island probably occurredonce, except for Miyake Island, where immigration has occurredat least twice. Copyright 2001 Annals of Botany Company AMOVA, Campanula microdonta Koidz., insular endemic plant, genetic diversity, population genetic structure, RAPD     

Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic

Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact.     

Spiders on a Hot Volcanic Roof: Colonisation Pathways and Phylogeography of the Canary Islands Endemic Trap-Door Spider Titanidiops canariensis (Araneae,Idiopidae)

Studies conducted on volcanic islands have greatly contributed to our current understanding of how organisms diversify. The Canary Islands archipelago, located northwest of the coast of northern Africa, harbours a large number of endemic taxa. Because of their low vagility, mygalomorph spiders are usually absent from oceanic islands. The spider Titanidiops canariensis, which inhabits the easternmost islands of the archipelago, constitutes an exception to this rule. Here, we use a multi-locus approach that combines three mitochondrial and four nuclear genes to investigate the origins and phylogeography of this remarkable trap-door spider. We provide a timeframe for the colonisation of the Canary Islands using two alternative approaches: concatenation and species tree inference in a Bayesian relaxed clock framework. Additionally, we investigate the existence of cryptic species on the islands by means of a Bayesian multi-locus species delimitation method. Our results indicate that T. canariensis colonised the Canary Islands once, most likely during the Miocene, although discrepancies between the timeframes from different approaches make the exact timing uncertain. A complex evolutionary history for the species in the archipelago is revealed, which involves two independent colonisations of Fuerteventura from the ancestral range of T. canariensis in northern Lanzarote and a possible back colonisation of southern Lanzarote. The data further corroborate a previously proposed volcanic refugium, highlighting the impact of the dynamic volcanic history of the island on the phylogeographic patterns of the endemic taxa. T. canariensis includes at least two different species, one inhabiting the Jandia peninsula and central Fuerteventura and one spanning from central Fuerteventura to Lanzarote. Our data suggest that the extant northern African Titanidiops lineages may have expanded to the region after the islands were colonised and, hence, are not the source of colonisation. In addition, T. maroccanus may harbour several cryptic species.     

Blitzkrieg in a Marine Invasion: Caulerpa racemosa var. cylindracea (Bryopsidales, Chlorophyta) Reaches the Canary Islands (North-East Atlantic)

On the basis of morphological and genetic studies (rDNA ITS1, 5.8S, ITS2, and a 18S rDNA intron), we confirm here that Caulerpa racemosa var. cylindracea (Sonder) Verlaque, Huisman et Boudouresque, a southwestern Australian taxon recently introduced into the Mediterranean Sea also occurs in the Canary Islands. This is the first report of C. racemosa var. cylindracea in the Atlantic. It was observed for the first time in the Canary Archipelago in 1997–1998. The speed and regional scale of expansion (north Atlantic Ocean and the Mediterranean Sea) of this invasive species appear to be among the most dramatic ever recorded. The possible outcome of this introduction in the Atlantic is discussed.     

Helminths of the wild rabbit (Oryctolagus cuniculus) in Macaronesia

Two hundred and four rabbits from 8 Macaronesian islands (Pico, San Jorge, San Miguel, Terceira, and Flores from Azores Archipelago; Tenerife and Alegranza from Canary Islands; and Madeira from Madeira Archipelago) were examined for helminth parasites between 1995 and 2000. Three species of cestodes, Taenia pisiformis (larvae), Andrya cuniculi, and Mosgovoyia ctenoides, and 5 species of nematodes, Trichuris leporis, Graphidium strigosum, Trichostrongylus retortaeformis, Passalurus ambiguus, and Dermatoxys hispaniensis, were identified. Only 3 species (M. ctenoides, T. retortaeformis, and P. ambiguus) were regularly distributed over the 3 archipelagos. Taenia pisiformis was not collected in Madeira, nor was A. cuniculi in the Azores and G. strigosum in the Canary Islands. Trichuris leporis and D. hispaniensis were only found in Madeira. Significant differences in the general prevalence of the nematodes G. strigosum and T. retortaeformis were detected between Azores and Madeira. The prevalence of T. retortaeformis differs significantly between the Azores and the Canaries and that of P. ambiguus was higher in Madeira than in Azores and Canaries. The helminth richness found in the wild rabbit in these Macaronesian archipelagos was very low compared with the Palearctic helminth fauna of this host. The wild rabbit was introduced from the Iberian Peninsula into different Macaronesian islands. Helminths introduced with Oryctolagus cuniculus into these islands also are commonly found in Iberian wild rabbits, which are excellent colonizers, as demonstrated in this study.     

Phylogeography of a pan-Atlantic abyssal protobranch bivalve: implications for evolution in the Deep Atlantic

The deep sea is a vast and essentially continuous environment with few obvious barriers to gene flow. How populations diverge and new species form in this remote ecosystem is poorly understood. Phylogeographical analyses have begun to provide some insight into evolutionary processes at bathyal depths (<3000 m), but much less is known about evolution in the more extensive abyssal regions (>3000 m). Here, we quantify geographical and bathymetric patterns of genetic variation (16S rRNA mitochondrial gene) in the protobranch bivalve Ledella ultima, which is one of the most abundant abyssal protobranchs in the Atlantic with a broad bathymetric and geographical distribution. We found virtually no genetic divergence within basins and only modest divergence among eight Atlantic basins. Levels of population divergence among basins were related to geographical distance and were greater in the South Atlantic than in the North Atlantic. Ocean‐wide patterns of genetic variation indicate basin‐wide divergence that exceeds what others have found for abyssal organisms, but considerably less than bathyal protobranchs across similar geographical scales. Populations on either side of the Mid‐Atlantic Ridge in the North Atlantic differed, suggesting the Ridge might impede gene flow at abyssal depths. Our results indicate that abyssal populations might be quite large (cosmopolitan), exhibit only modest genetic structure and probably provide little potential for the formation of new species.     

Screening of Trypanosoma brucei gambiense in Domestic Livestock and Tsetse Flies from an Insular Endemic Focus (Luba,Equatorial Guinea)

Background

Sleeping sickness is spread over 36 Sub-Saharan African countries. In West and Central Africa, the disease is caused by Trypanosoma brucei gambiense, which produces a chronic clinical manifestation. The Luba focus (Bioko Island, Equatorial Guinea) has not reported autochthonous sleeping sickness cases since 1995, but given the complexity of the epidemiological cycle, the elimination of the parasite in the environment is difficult to categorically ensure.

Methodology/Principal Findings

The aim of this work is to assess, by a molecular approach (Polymerase Chain Reaction, PCR), the possible permanence of T. b. gambiense in the vector (Glossina spp.) and domestic fauna in order to improve our understanding of the epidemiological situation of the disease in an isolated focus considered to be under control.The results obtained show the absence of the parasite in peridomestic livestock but its presence, although at very low rate, in the vector. On the other hand, interesting entomological data highlight that an elevated concentration of tsetse flies was observed in two out of the ten villages considered to be in the focus.

Conclusions

These findings demonstrate that even in conditions of apparent control, a complete parasite clearance is difficult to achieve. Further investigations must be focused on animal reservoirs which could allow the parasites to persist without leading to human cases. In Luba, where domestic livestock are scarcer than other foci in mainland Equatorial Guinea, the epidemiological significance of wild fauna should be assessed to establish their role in the maintenance of the infection.     

Phylogeography of the Bothrops jararaca complex (Serpentes: Viperidae): past fragmentation and island colonization in the Brazilian Atlantic Forest

The Brazilian Atlantic Forest is one of the world's major biodiversity hotspots and is threatened by a severe habitat loss. Yet little is known about the processes that originated its remarkable richness of endemic species. Here we present results of a large-scale survey of the genetic variation at the mitochondrial cytochrome b gene of the pitviper, jararaca lancehead (Bothrops jararaca), and two closely related insular species (Bothrops insularis and Bothrops alcatraz), endemic of this region. Phylogenetic and network analyses revealed the existence of two well-supported clades, exhibiting a southern and a northern distribution. The divergence time of these two phylogroups was estimated at 3.8 million years ago, in the Pliocene, a period of intense climatic changes and frequent fragmentation of the tropical rainforest. Our data also suggest that the two groups underwent a large size expansion between 50,000 and 100,000 years ago. However, the southern group showed a more marked signal of population size fluctuation than the northern group, corroborating evidences that southern forests may have suffered a more pronounced reduction in area in the late Pleistocene. The insular species B. alcatraz and B. insularis presented very low diversity, each one sharing haplotypes with mainland individuals placed in different subclades. Despite their marked morphological and behavioural uniqueness, these two insular species seem to have originated very recently and most likely from distinct costal B. jararaca populations, possibly associated with late Pleistocene or Holocene sea level fluctuations.     

Latitudinal Environmental Niches and Riverine Barriers Shaped the Phylogeography of the Central Chilean Endemic Dioscorea humilis (Dioscoreaceae)

The effects of Pleistocene glaciations and geographical barriers on the phylogeographic patterns of lowland plant species in Mediterranean-climate areas of Central Chile are poorly understood. We used Dioscorea humilis (Dioscoreaceae), a dioecious geophyte extending 530 km from the Valparaíso to the Bío-Bío Regions, as a case study to disentangle the spatio-temporal evolution of populations in conjunction with latitudinal environmental changes since the Last Inter-Glacial (LIG) to the present. We used nuclear microsatellite loci, chloroplast (cpDNA) sequences and environmental niche modelling (ENM) to construct current and past scenarios from bioclimatic and geographical variables and to infer the evolutionary history of the taxa. We found strong genetic differentiation at nuclear microsatellite loci between the two subspecies of D. humilis, probably predating the LIG. Bayesian analyses of population structure revealed strong genetic differentiation of the widespread D. humilis subsp. humilis into northern and southern population groups, separated by the Maipo river. ENM revealed that the ecological niche differentiation of both groups have been maintained up to present times although their respective geographical distributions apparently fluctuated in concert with the climatic oscillations of the Last Glacial Maximum (LGM) and the Holocene. Genetic data revealed signatures of eastern and western postglacial expansion of the northern populations from the central Chilean depression, whereas the southern ones experienced a rapid southward expansion after the LGM. This study describes the complex evolutionary histories of lowland Mediterranean Chilean plants mediated by the summed effects of spatial isolation caused by riverine geographical barriers and the climatic changes of the Quaternary.     

A Complex Evolutionary History in a Remote Archipelago: Phylogeography and Morphometrics of the Hawaiian Endemic Ligia Isopods

Compared to the striking diversification and levels of endemism observed in many terrestrial groups within the Hawaiian Archipelago, marine invertebrates exhibit remarkably lower rates of endemism and diversification. Supralittoral invertebrates restricted to specific coastal patchy habitats, however, have the potential for high levels of allopatric diversification. This is the case of Ligia isopods endemic to the Hawaiian Archipelago, which most likely arose from a rocky supralittoral ancestor that colonized the archipelago via rafting, and diversified into rocky supralittoral and inland lineages. A previous study on populations of this isopod from Oʻahu and Kauaʻi revealed high levels of allopatric differentiation, and suggested inter-island historical dispersal events have been rare. To gain a better understanding on the diversity and evolution of this group, we expanded prior phylogeographic work by incorporating populations from unsampled main Hawaiian Islands (Maui, Molokaʻi, Lanaʻi, and Hawaiʻi), increasing the number of gene markers (four mitochondrial and two nuclear genes), and conducting Maximum likelihood and Bayesian phylogenetic analyses. Our study revealed new lineages and expanded the distribution range of several lineages. The phylogeographic patterns of Ligia in the study area are complex, with Hawaiʻi, Oʻahu, and the Maui-Nui islands sharing major lineages, implying multiple inter-island historical dispersal events. In contrast, the oldest and most geographically distant of the major islands (Kauaʻi) shares no lineages with the other islands. Our results did not support the monophyly of all the supralittoral lineages (currently grouped into L. hawaiensis), or the monophyly of the terrestrial lineages (currently grouped into L. perkinsi), implying more than one evolutionary transition between coastal and inland forms. Geometric-morphometric analyses of three supralittoral clades revealed significant body shape differences among them. A taxonomic revision of Hawaiian Ligia is warranted. Our results are relevant for the protection of biodiversity found in an environment subject to high pressure from disturbances.     

Phylogeography and population history of Atlantic mackerel (Scomber scombrus L.): a genealogical approach reveals genetic structuring among the eastern Atlantic stocks

Despite the resolving power of DNA markers, pelagic and migratory marine fish species generally show very little geographical population structuring. In mackerel (Scomber scombrus L.) population differentiation has been detected only at a transatlantic scale. By applying two regions in mitochondrial DNA (mtDNA) (D-loop and cytochrome b (cytb)) in combination with genealogical and frequency-based statistical approaches, our data suggest population differentiation among eastern Atlantic spawning stocks. In contrast, and indicative of homing behaviour, no genetic structuring was observed among shoals of individuals outside the spawning season. Among spawning stocks, mtDNA D-loop sequences detected differentiation within the eastern Atlantic, while the cytb gene detected transatlantic differentiation. The impact of recurrent events (e.g. gene flow restricted by isolation by distance) and historic events (e.g. population range expansions) among spawning stocks was investigated applying a nested cladistic analysis of geographical distribution of cytb haplotype lineages. In the eastern Atlantic, historical population range expansion, presumably in connection with recolonization of northern areas after the last glaciation, is suggested to be the main factor determining mtDNA lineage distribution. This was supported by estimates of mtDNA nucleotide diversity, where the highest diversity was observed for the stock spawning in the Bay of Biscay, for which the size estimate is only 15% of the largest stock (Celtic Sea). In addition to revealing population differentiation, our data demonstrate the importance of sampling strategy and the power of applying statistical methods addressing both ongoing and historical population processes.     

Phylogeography of a facultatively migratory dragonfly, Libellula quadrimaculata (Odonata: Anisoptera)

The biogeography of a widely distributed dragonfly (Libellula quadrimaculata) was examined via a phylogenetic analysis of 416 bp of the mitochondrial cytochrome oxidase I subunit (COI). Phylogenetic analyses under parsimony and minimum evolution produced trees with similar topologies, and revealed strong support for three clades corresponding to populations in Asia, Europe and North America. However, resolution was poor within clades, and genetic distances between populations within continents was quite low (1–2%). Several populations of this species are known to engage in periodic mass migrations, and it is possible that introgression from gene flow due to the mobility of this species has obscured phylogenetic patterns within continents. I was unable to test for phylogenetic patterns coincident with historical glacial refugia given the lack of phylogenetic patterns within continents. However, given that some sequence divergence was observed between populations within continents, it is possible that phylogenetic patterns exist, and subsequent studies should make use of larger data sets, and molecular data from faster evolving genes. Despite the propensity for periodic, short distance migrations in L. quadrimaculata, gene flow appears to be limited and does not influence the phylogenetic relationships of populations between continents.     

Phylogeography of the Wabash pigtoe, Fusconaia flava (Rafinesque, 1820) (Bivalvia: Unionidae)

Reconstructing the phylogeographic patterns of widely distributedand common freshwater mussel species (Bivalvia: Unionidae) mayprovide insight into unionid evolution and speciation. The Wabashpigtoe, Fusconaia flava, is currently recognized as a single,polytypic species that is widely distributed and common throughoutthe Mississippi River drainage and parts of the Canadian Interior,Great Lakes and Gulf Coast drainages. Sequence analysis of themitochondrial COI gene revealed two divergent (3.43%) clades.Clade A consisted of specimens located throughout the upperand lower Mississippi River drainage and in the Red River (Canada)and Lake Erie drainages and all F. cerina specimens. All haplotypeswithin clade A differed by three (0.55%) or fewer nucleotidesubstitutions from the most widely distributed and abundanthaplotype, F1. Clade B, consisting of specimens located in thefar western portion of the species' range, may comprise an undescribedspecies. There was no evidence of genetic differentiation amongF. flava inhabiting headwater and intermediate-sized river localitiesof the Muskingum River system and large river localities ofthe nearby Ohio River. The divergence among F. flava haplotypescomprising clade A (0.18–1.10%) was similar to the divergencebetween the F. cerina haplotypes and the F. flava haplotypescomprising clade A (0–1.10%). This study illustrates theimportance of accessing genetic diversity across the distributionof a polytypic species. Additional analyses based on a combinationof morphology and genetics are needed to determine the taxonomicstatus of clade B and to strengthen our understanding of therelationship between F. flava and F. cerina. (Received 28 May 2007; accepted 13 August 2007)     

Phylogeography of the genus Epiplatys (Aplocheiloidea: Cyprinodontiformes)

There are six major genera of aplocheiloid killifishes endemic to West Africa. Five of these are largely restricted to the two major blocks of rainforest. Two are found within the Eastern rainforest block (Nigeria to the central Congo) while three are found within the Western rainforest block (Sierra Leone to Togo). The sixth genus (Epiplatys) has a range that exceeds that of the combined area of the other five genera. Phylogenetically this genus is related to the Western rainforest taxa. Phylogeographic analysis of this genus suggests that it escaped the confines of the Western block by first expanding into lowland habitats exposed after a sea level drop and then dispersed along coastal habitats to the east. One lineage managed to penetrate the interior of the Eastern rainforest block and one derivative of this lineage penetrated the Congo basin. A second route out of the Western rainforest block was to the north through what is now savannah habitat. The greater phylogeographic range of Epiplatys is hypothesized to be due to retention of ancestral morphology related to a greater adaptability compared to the other five genera.