Genetic diversity in Atlantic Forest trees: fragmentation effects on Astronium graveolens (Anacardiaceae) and Metrodorea nigra (Rutaceae), species with distinct seed dispersal strategies

We explore the genetic structure and variability in autochorous Metrodorea nigra (Rutaceae) and anemochorous Astronium graveolens (Anacardiaceae), two species affected by deforestation in the Atlantic Forest of Brazil. The effects of deforestation and the depletion of the habitat within the remaining patches of forest are evaluated by comparing the variability between saplings and adults of each of these two species. The results indicate that the depletion of forest land and the deteriorating condition of the remaining fragments of forest may reduce the level of endogamous breeding in wind‐dispersed species. In autochorous species, the fragmentation of forest land has less notable effects on genetic attributes, but pollen flow could be decreased as a result of the reduced number of insects flying between the forest remnants. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 326–336.     

First record of the taxon Echinopsyllus (Copepoda,Harpacticoida, Ancorabolidae) from the deep sea of Campos Basin,Brazil, with the description of three new species and their contribution to phylogenetic analysis

New species assignable to the formerly monotypic genus Echinopsyllus (Copepoda, Harpacticoida, Ancorabolidae) are described from the continental slope of Campos Basin off Brazil in the south‐western Atlantic. Echinopsyllus brasiliensis sp. nov. , Echinopsyllus nogueirae sp. nov. , and Echinopsyllus grohmannae sp. nov. differ from Echinopsyllus normani Sars, 1909 in the cephalothorax having two instead of three pairs of lateral processes, first pair of dorsal cephalothoracic processes being smaller than second pair, second pair of dorsal cephalothoracic processes branched, and segmentation and setation of the swimming legs. The discovery of new species of Echinopsyllus extends the distributional range of the genus to the southern hemisphere and is further evidence for the formerly unexpected wide genus‐level distribution of Ancorabolidae in the world's oceans. The phylogenetic position of Echinopsyllus within Ancorabolinae is discussed. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 52–78.     

DNA sequences corroborate Soesiladeepakius as a non‐salticoid genus of jumping spiders: placement with lapsiines,phylogeny, and description of six new species (Araneae,Salticidae)

Species of the Amazonian jumping spider genus Soesiladeepakius Makhan are confirmed as non‐salticoids. Sequences of nuclear (28S, Actin) and mitochondrial (16S through NADH dehydrogenase subunit I, ‘16S‐ND1’) gene regions, analysed under parsimony and maximum likelihood, placed the genus within the lapsiines, closely related to Galianora Maddison. Additionally, six new species of this genus are herein described, namely Soesiladeepakius lyra sp. nov. , Soesiladeepakius retroversus sp. nov. , Soesiladeepakius arthrostylus sp. nov. , Soesiladeepakius gasnieri sp. nov. , Soesiladeepakius biarmatus sp. nov. , and Soesiladeepakius uncinatus sp. nov. , all from the Amazon region in Brazil. To test the monophyly of Soesiladeepakius within lapsiines, a cladistic analysis was carried out using a data matrix comprising 24 morphological characters scored for 12 taxa. The analysis resulted in two equally parsimonious trees of 29 steps. One of these trees is used to discuss the relationships among the species of Soesiladeepakius and character evolution. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 274–295.     

Revision of the New World genus Quichuana Knab, 1913 (Diptera: Syrphidae), including descriptions of 24 new species

The species of the New World syrphid genus, Quichuana Knab, 1913 (Diptera: Syrphidae: Eristalini), are revised and the genus is re‐diagnosed. Twenty‐four new species are described, bringing the total number considered valid to 48. New species were mostly reared from Bolivia, Brazil, Costa Rica, El Salvador, Mexico, Peru, Trinidad, and Venezuela. The male of Quichuana picadoi is described for the first time. Quichuana championi is proposed as a synonym of Quichuana cincta, Quichuana aurata as a synonym of Quichuana angustiventris, and Quichuana sepiapennis as a synonym of Quichuana calathea. Quichuana inca var. brevicera is raised to specific status. Lectotypes are designated for Helophilus auratus, Quichuana bezzii, Quichuana fasciata, and Quichuana parisii. A species‐level identification key for both males and females is provided. Male genitalia of 18 species are illustrated. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 72–131.     

A new genus and species of rodent from the Brazilian Atlantic Forest (Rodentia: Cricetidae: Sigmodontinae: Oryzomyini), with comments on oryzomyine biogeography

We describe in this paper a new genus and species of cricetid rodent from the Atlantic Forest of Brazil, one of the most endangered eco‐regions of the world. The new form displays some but not all synapomorphies of the tribe Oryzomyini, but a suite of unique characteristics is also observed. This new forest rat possesses anatomical characteristics of arboreal taxa, such as very developed plantar pads, but was collected almost exclusively in pitfall traps. Phylogenetic analyses of morphological (integument, soft tissue, cranial, and dental characters) and molecular [nuclear – Interphotoreceptor retinoid binding protein (Irbp) – and mitochondrial – cytochrome b– genes] datasets using maximum likelihood and cladistic parsimony approaches corroborate the inclusion of the new taxon within oryzomyines. The analyses also place the new form as sister species to Eremoryzomys polius, an Andean rat endemic to the Maranon valley. This biogeographical pattern is unusual amongst small terrestrial vertebrates, as a review of the literature points to few other similar examples of Andean–Atlantic Forest pairings, in hylid frogs, Pionus parrots, and other sigmodontine rodents. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 357–390.     

Historical biogeography of the Brazilian Atlantic forest and the Carnaval–Moritz model of Pleistocene refugia: what do phylogeographical studies tell us?

The present study uses published phylogeographical studies to test the Carnaval–Moritz (CM) model of forest dynamics in the Atlantic forest of Brazil. The model predicts that a large forested area in the north–central region of this biome has remained stable during the last glacial maximum, and only relicts in its current southernmost distributions. All available sequences for phylogeographical studies on vertebrates on the Atlantic forest were obtained from GenBank. All datasets consisted of mitochondrial sequences and were submitted to the same analyses, including time of divergence and migration rates between phylogeographical lineages, as well as historical demography analyses, including neutrality tests and N_e estimates. The species studied showed different degrees of phylogeographical structure. Two contact zones are defined: one very heterogeneous in south‐east Brazil that was largely congruent with the CM model and one around the Doce river further north. Population genetics analyses showed a smaller effective number on southern population, and most of these southern populations showed evidence for recent demographic expansion. These features are also in agreement with the CM model. Additionally, divergence/expansion events dated back to the Pleistocene epoch in all but one organism. According to hierarchical approximate Bayesian computation analysis, most of the data can be attributed to a single event. The results highlight the need for more finescale studies in the Atlantic forest. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 499–509.     

Taxonomic review of genus Sooretamys Weksler,Percequillo & Voss (Rodentia: Cricetidae: Sigmodontinae): an integrative approach

Sooretamys is a monotypic genus of the family Cricetidae, subfamily Sigmodontinae, that is distributed throughout eastern South America in the Atlantic Forest Biome, including Argentina, Brazil, and Paraguay. The taxonomic history of the forms associated with this genus is long and relatively complex, and few studies have evaluated the taxonomic problems of this genus. To this end, our goal was to describe the degree and geographical pattern of morphological and molecular variation in this genus to test the current hypothesis that the genus is monotypic, and, as a consequence, to determine the status of the nominal forms associated with Sooretamys. Accordingly, we employed morphometric, morphological, and molecular tools, according to an integrative taxonomy approach. The results show that some level of morphometric discontinuity is present between the individuals from Paraguay and those from adjacent localities in Brazil and Argentina; sharp discontinuities were not observed in qualitative traits. Molecular analyses of the mitochondrial cytochrome b gene showed that the Paraguayan populations have some degree of genetic differentiation, but the haplotypic variants do not form a monophyletic group. Thus, the evidence so far suggests a difference in the genes and morphology of the Paraguayan population, but there is no consistent resolution (e.g. lack of monophyly) to show that specimens from Paraguay represent a distinct population that would merit taxonomic recognition. Thus, we recognize a single species within the genus Sooretamys, named Sooretamys angouya. The pattern of morphological and genetic differentiation of Sooretamys could be the result of divergence with gene flow. However, our data also correspond in some aspects with the model advanced by Carnaval & Moritz, which claims the existence of stable Atlantic Forest areas where the forest biota persisted during the Quaternary climatic fluctuations. Whatever process has occurred, S. angouya represents one species with a complex evolutionary history, and the analysis of additional samples would be welcome to further elucidate the process of diversification of this taxon. © 2014 The Linnean Society of London     

A reconsideration of the Lower Guinean species of Sericanthe (Rubiaceae,Coffeeae), with four new species from Cameroon and Gabon

The genus Sericanthe was established and its species were revised 30 years ago by one of the authors. Intensive recent botanical collecting in Lower Guinea (mainly southern Cameroon, Equatorial Guinea and Gabon) has made a reconsideration of species in this area necessary. Revision of the newly collected Lower Guinean herbarium specimens of Sericanthe (twice as many as were available at the time of the first revision) has brought four new species to light, namely S. gabonensis and S. mpassa from Gabon, S. lowryana from Cameroon and S. rabia from Cameroon and Gabon. Distributional data are much augmented, and distributional maps of all species from the area are provided. Four species were reported to be newly recorded for at least one country. The occurrence of the novelties in the main diversity centre of the genus is discussed in the context of the chorology of the entire genus Sericanthe. A first estimation of the conservation status for the new species is given. A synopsis of the genus Sericanthe in Lower Guinea with a taxonomic key is provided. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 530–554.     

Revision and phylogeny of the bee genus Paratetrapedia Moure,with description of a new genus from the Andean Cordillera (Hymenoptera,Apidae, Tapinotaspidini)

The bee genus Paratetrapedia represents a commonly collected group of bees and is especially diverse in forested areas of the Neotropics. Its taxonomy has remained poorly understood because of a lack of modern revisionary work and numerous species described as Tetrapedia whose type specimens have not been re‐examined in recent times. Here, a comprehensive study was carried out to review the taxonomy of the genus Paratetrapedia and to investigate cladistically the relationships amongst its species. Eighteen new species of Paratetrapedia are described, giving a total of 32 species in the genus. A phylogenetic analysis of the species of Paratetrapedia was carried out using 61 morphological characters for 41 terminal taxa. The phylogenetic results confirmed the monophyly of Paratetrapedia and allowed the recognition of five species groups: the lugubris, moesta, bicolor, lineata, and flavipennis groups. Nasutopedia gen. nov. , recognized as the sister group of Paratetrapedia and with its distribution restricted to the western forested portions of the Andean highlands, is proposed based on distinct morphology, its placement in the phylogenetic tree, and biogeographical patterns. Species of Paratetrapedia are especially diverse in the Amazon Forest; the eastern Brazilian Atlantic Forest contains four endemic species, and one species is endemic to the Cerrado of central Brazil. Paratetrapedia shows a biogeographical pattern similar to other Neotropical groups of bees and birds, with wide distribution and high diversity in lowland forests and whose sister taxon occurs on highlands of north‐western portions of the Andean cordillera. Identification keys for males and females of all species are provided, as well as distribution maps and illustrations of general external morphology and genitalia. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 351–442.     

A taxonomic revision of Encyclia (Orchidaceae: Laeliinae) in Costa Rica

A taxonomic revision of Encyclia (Orchidaceae) in Costa Rica is presented. The taxonomic history of the genus and its phylogenetic position are discussed. Characters of vegetative and floral morphology are described and their taxonomic significance is discussed. The genus is treated as comprising nine species in the country and a key to species is provided. Each taxon is described on the basis of Costa Rican material, illustrated in a composite plate, and its distribution within the country is assessed. Distribution maps for all the taxa are given. Overall distribution, derivation of name, synonymy, notes on species ecology and diagnostic features are presented for each taxon. The names Encyclia tonduziana and Epidendrum mooreanum are typified. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 395–448.     

A molecular phylogenetic appraisal of the systematics of the Aglaopheniidae (Cnidaria: Hydrozoa,Leptothecata) from the north‐east Atlantic and west Mediterranean

The hydrozoan family Aglaopheniidae (Cnidaria) is widespread worldwide and contains some of the most easily recognizable hydroids because of their large colony size and characteristic microscopic structure. The systematics of the group has, however, been controversial and dedicated molecular analyses are lacking. We therefore analysed existing and new 16S rRNA sequences of Aglaopheniidae, in a total of 98 16S sequences corresponding to 25 putative species (25 nominal and three undescribed) from seven genera. The monophyly of the subfamilies Gymnangiinae and Aglaopheniinae, and tribes Aglaopheniini and Cladocarpini were not verified with 16S sequence data. The genera Gymnangium and Aglaophenia can only be considered valid if both Gymnangium gracicaule and Aglaophenia latecarinata are removed from their respective genera. The phenotypically similar Cladocarpus and Streptocaulus are probably monophyletic and clearly distinct genetically. The genus Lytocarpia may be polyphyletic. The nominal species Aglaophenia pluma, Aglaophenia tubiformis, and Aglaophenia octodonta are probably conspecific, as are also the species Aglaophenia acacia and Aglaophenia elongata. The 16S data revealed the existence of two potentially unnamed species of Aglaophenia respectively from the Azores and Madeira. The phylogeographical structure of the taxa with the greatest representation of haplotypes from the north‐east Atlantic and Mediterranean, revealed the influence of Mediterranean waters in Madeira and the Azores, and gene flow between deep waters of the Mediterranean and Atlantic. The last glaciations in Europe may have caused genetic bottlenecks but also high intraspecific haplotype diversity. Finally, Macrorhynchia philippina was detected in samples from Madeira and possibly represents an invasive species. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 717–727.     

Goeppertia mendesiana sp. nov. (Marantaceae) from Bahia,Brazil, with a key to the species of Goeppertia with ornamented leaves in the Atlantic Forest of Brazil

Goeppertia mendesiana, a new species from the Atlantic Forest of Bahia, Brazil, is described and illustrated. It resembles G. widgrenii (Körn.) Borchs. & Suárez, but differs from that species by its villose petioles and peduncles (vs glabrous in G. widgrenii) and by the absence of bracteoles and interphylls, a rare feature in the genus. The ecology, distribution and conservation status of the new species is presented, along with a key to the species of Goeppertia with ornamented leaves in the Atlantic Forest of Brazil.     

Genetic variation in natural populations of Anthurium sinuatum and A. pentaphyllum var. pentaphyllum (Araceae) from north‐east Brazil using AFLP molecular markers

Genetic variation was investigated using AFLP markers in 12 populations of Anthurium sinuatum and A. pentaphyllum var. pentaphyllum (Araceae) in north‐east Brazil, Amazonia and the Brazilian Atlantic forest. Two unique genetic patterns characterized the populations of A. sinuatum as a group, but no correlation between genetic and geographical interpopulation distance was found; the Amazonian population was not separated from that in Ceará. The isolated Ceará brejo populations of A. sinuatum were genetically distinct, but genetic diversity levels were similar to populations elsewhere, with no evidence of genetic erosion. Anthurium pentaphyllum populations were significantly different from each other; Bayesian genetic structural analysis found no common genetic pattern, but revealed genetic clusters unique to subgroups and individual populations in the Atlantic forest and French Guiana. Anthurium pentaphyllum and A. sinuatum can be distinguished genetically, but individuals of both species formed intermediate genetic clusters that blurred their distinction. We suggest that genetic mixing of A. sinuatum and A. pentaphyllum has occurred in north‐east Brazil, possibly connected with cycles of humid forest expansion. The weak genetic structure in A. sinuatum is consistent with the natural fragmentation of continuous forest areas, possibly during the Holocene. This study highlights the scientific importance of the highly threatened brejo forests for tropical American biogeography. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 88–105.     

A new genus of African Acrometopini (Tettigoniidae: Phaneropterinae) based on morphology,chromosomes, acoustics,distribution, and molecular data,and the description of a new species

A new genus, Altihoratosphaga, is erected for species formerly assigned to Horatosphaga Schaum, 1853, and a new species is described. Four species are included in Altihoratosphaga: Altihoratosphaga nomima (Karsch, 1896), Altihoratosphaga montivaga ( Sjöstedt, 1909 ), Altihoratosphaga nou (Hemp, 2007) and Altihoratosphaga hanangensis sp. nov. All four species are restricted to Tanzanian localities, and, except for A. nomima, for which no ecological data are available, are confined to montane forest habitats. Data on ecology, acoustics, chromosomes, and molecular relationships are provided, as well as a key to Altihoratosphaga species. The present‐day distribution of Altihoratosphaga species suggests former migration events at times when wetter and colder climatic fluctuations favoured connections between montane forest communities, which today are isolated, enabling flightless taxa such as Altihoratosphaga and Monticolaria to spread. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 66–82.     

Patterns of diversification in two species of short‐tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests

The small‐sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 527–539.