Phylogenetic affinities and species limits within the genus Megadontomys (Rodentia: Cricetidae) based on mitochondrial sequence data

The evolutionary history of the genus Megadontomys, a group of mice allopatrically distributed along the cool‐humid forest in the highlands of México, is controversial. In this study, we examined phylogenetic relationships within the genus using sequences data from the complete mitochondrial cytochrome b gene. This information also allowed us to corroborate species limits, geographic boundaries of taxonomic entities and assess genetic variation within each taxon. The results of the phylogenetic analyses based on maximum likelihood, Bayesian inference and maximum parsimony were largely congruent in that M. nelsoni and M. thomasi were more closely related relative to M. cryophilus. These results are concordant with previous studies based on morphology and allozyme variation. However, testing of the alternative hypothesis of a closer evolutionary affinity between M. nelsoni–M. cryophilus did not produce a significantly less likely tree. The lack of unambiguous support towards one of these previously proposed contending hypotheses is congruent with the alternative scenario of an almost simultaneous diversification of the three species. Application of the phylogenetic species concept and the genetic species concept supports the recognition of three distinct taxonomic entities at the specific level. M. nelsoni inhabits the Sierra Madre Oriental (Hidalgo, Veracruz, and Puebla) including the Sierra Mazateca (Oaxaca); M. cryophilus is restricted to the Sierra de Juárez (Oaxaca); and M. thomasi occurs in portions of the Sierra Madre del Sur (Guerrero) and the Sierra Mixteca (Oaxaca). Our data show that M. thomasi is formed by two genetically distinct lineages that potentially may represent distinct Evolutionary Significant Units.     

Molecular systematics,taxonomy and biogeography of the genus Cavia (Rodentia: Caviidae)

Phylogenetic analyses were conducted on cytochrome b sequence data of the most geographically and taxonomically broad sampling of Cavia taxa to date. Primary objectives included providing the first extensive molecular phylogenetic framework for the genus, testing the taxonomic and systematic hypotheses of previous authors and providing insight into the evolutionary and biogeographic history of the genus. Support was found for the morphologically defined species C. aperea, C. tschudii, C. magna and C. fulgida and the taxonomic placement of taxa previously subject to conflicting taxonomic opinions (e.g. C. nana, C. anolaimae and C. guianae) was further resolved. Additionally, we elevate the Ecuadorian C. a. patzelti to species status, restrict the distributional limits and suggest taxonomic affiliations of some C. tschudii subspecies, and provide strong evidence for the geographic origin of guinea pig domestication. Finally, we provide an estimated evolutionary timeline for the genus Cavia, which appears to extend well into the late Miocene.     

The molecular phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae) clarifies rodent host–hantavirus associations

Several species of the genus Oligoryzomys are natural hosts of different hantavirus genotypes affecting humans. The systematics of the genus is confusing, which complicates the identification of the rodent host and hence the potential endemic areas of hantavirus pulmonary syndrome. In this study, we analyse molecular data to infer phylogenetic relationships among Central and South American specimens of Oligoryzomys, and compare our results with previously published data on karyotypic, geographic distribution and host–virus associations to solve contradictory taxonomic reports. We identified 25 clades, each one corresponding to a different putative species. The phylogenetic trees show that Oligoryzomys longicaudatus is strongly related to the Oligoryzomys flavescens complex, which comprises four clades; Oligoryzomys nigripes is related to Oligoryzomys stramineus, Oligoryzomys vegetus is related to Oligoryzomys fulvescens from Central America, and Oligoryzomys brendae is the sister species of Oligoryzomys aff. destructor. We identified the following rodent host–hantavirus genotype relationships: O. longicaudatus–Andes; O. flavescens ‘West'–Bermejo; O. flavescens ‘East'–Lechiguanas; O. nigripes–Juquitiba; Oligoryzomys microtis–Rio Mamore and Rio Mamore‐3; Oligoryzomys chacoensis–Oran; Oligoryzomys costaricencis–Choclo; Oligoryzomys delicatus–Maporal; Oligoryzomys utiaritensis–Castelo dos Sonhos; Oligoryzomys sp. RT2012–Rio Mamore‐4; Oligoryzomys sp. (and not Oligoryzomys fornesi)–Anajatuba. This work, besides contributing to the development of prevention programmes for hantavirus epidemiology in Latin America, represents a comprehensive update of the systematics of the genus Oligoryzomys. © 2014 The Linnean Society of London     

Phylogenetic relationships of the sea eagles (genus Haliaeetus): reconstructions based on morphology, allozymes and mitochondrial DNA sequences

The relationships of eight extant species of sea eagles (genus Haliaeetus ) and some potentially related Accipitrid genera were investigated. A phylogenetic hypothesis is developed based on morphological characters and allozyme data, which is then contrasted with a reconstruction based on 1071 nucleotides of mitochondrial DNA (cytochrome b and part of one tRNA gene). Phylogenies derived from the three data sets are largely congruent, although several aspects are supported by only one kind of evidence (but not contradicted by the others). Only with regard to the position of south-east Asian H. leucogaster and its closely related sister species H. sanfordi was there conflict between allozyme and mtDNA data. The position of H. pelagicus relative to H. leucoryphus or H. albicilla/leucocephalus could not be resolved with the mtDNA sequence data, suggesting that some speciation events occurred in relatively quick succession during the early Pliocene or late Miocene periods. Available evidence suggests that extant sea eagles originated at tropical latitudes, the northernmost species appearing most derived.     

Evolutionary diversification of spiny rats (genus Trinomys, Rodentia: Echimyidae) in the Atlantic Forest of Brazil

Phylogenetic and phylogeographic relationships within and among species of the Atlantic Forest spiny rat Trinomys (family Echimyidae) were examined using cytochrome b sequence data. Levels of sequence divergence among species of Trinomys are as high as those found among taxa of echimyids that are recognized as different genera. Trinomys contains three distinct monophyletic clades that show a striking concordance with vegetational distribution. Haplotypes of clade 1 are distributed along the coastal margins of southeastern Brazil, following the moist tropical forest. Members of clade 2 are found in the semi-deciduous tropical forest. T. albispinus represents clade 3 and is found in a more xeric vegetation. Estimates of divergence times separating the three clades are very deep and range from 1.6 to 7.4 millions of years, predating the climatic fluctuations of the Pleistocene. Therefore, the proposed Late Pleistocene refugia in the Atlantic Forest cannot account for the divergence of the clades of Trinomys , but most likely shaped the modern distribution of species. The current taxonomy of this group does not reflect the diversity and phylogenetic relationships of the named species. However, morphological characters are congruent with the phylogeny uncovered by the molecular data. An extensive taxonomic rearrangement is suggested, reflecting phylogenetic relationships of monophyletic entities within the genus Trinomys , degree of sequence differences, and morphological diagnosability.     

Phylogenetic relationships among species of the genus Oligoryzomys (Rodentia,Cricetidae) from Central and South America

González‐Ittig, R. E., Salazar‐Bravo, J., Barquez, R. M. & Gardenal, C. N. (2010). Phylogenetic relationships among species of the genus Oligoryzomys (Rodentia, Cricetidae) from Central and South America. —Zoologica Scripta, 39, 511–526. The genus Oligoryzomys includes several species very similar in external morphology, which has resulted in a confusing specific taxonomy. Accurate species identification is particularly important because several species of Oligoryzomys act as natural hosts of hantaviruses affecting humans. Here, we assign specific status to individuals from a wide geographical area of Argentina and Chile using sequences of the mtDNA control region. We also compare cytochrome b sequences of 14 species recognized from Central and South America to infer the phylogenetic relationships within the genus. In addition, the results were analysed using available data on chromosome numbers, and the host–parasite relationships reported for the genus Hantavirus. We confirm the geographical distribution of Oligoryzomys longicaudatus (Argentina, Chile), Oligoryzomys nigripes (Argentina, Paraguay, Brazil), Oligoryzomys chacoensis (Argentina, Bolivia, Paraguay), Oligoryzomys fornesi (Argentina, Paraguay), Oligoryzomys destructor (Argentina, Bolivia) and Oligoryzomys microtis (Bolivia, Brazil). Oligoryzomys longicaudatus is strongly related to the Oligoryzomys flavescens complex, which comprises four clades; O. nigripes is closely related to Oligoryzomys stramineus, and Oligoryzomys vegetus, to Oligoryzomys fulvescens from Central America. Oligoryzomys chacoensis, O. destructor, O. fornesi, O. longicaudatus, O. microtis, O. nigripes, O. stramineus, Oligoryzomys moojeni, Oligoryzomys rupestris, O. fulvescens and O. vegetus are confirmed as valid species, whereas O. flavescens, Oligoryzomys magellanicus, Oligoryzomys griseolus, Oligoryzomys victus, Oligoryzomys andinus and Oligoryzomys arenalis need exhaustive revision. The sister species to all the remaining entities of the genus was O. microtis, suggesting an Amazonian origin for the genus.     

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.     

Phylogenetic relationships within the corbiculate Apinae (Hymenoptera) and the evolution of eusociality

We provide a comparison of 520 base pairs of the mitochondrial cytochrome b gene from exemplars of the Meliponini, the Apini, the Bombini and the Euglossini to determine the phylogenetic relationships within the corbiculate Apinae. Our results strongly suggest (91–97% according to bootstrap resampling) that the Meliponini and the Bombini are sister groups. This finding agrees with those of other molecular studies, but is discordant with previous hypotheses based on morphology and the combination of molecular and morphological data. If the Bombini and Meliponini are sister groups and reversal of advanced eusociality is unlikely, then advanced eusociality arose twice within this clade. However, if reversion of eusociality occurred, then it is not possible to discriminate between single or dual origins of advanced eusociality within this group.     

A new karyotype of Oligoryzomys (Sigmodontinae, Rodentia) from central Brazil

A new karyotype of the genus Oligoryzomys was described for specimens collected in Brazilian Cerrado in Tocantins and Goiás States. Conventional staining, G-, C-banding, and Ag-NOR staining techniques were used for describe this karyotype with 2n=70, AN=74 or 76. The chromosome complement, with the highest diploid number known among Oligoryzomys species, differs from all others previously reported. This small sized Oligoryzomys species can be differentiated from other Brazilian Oligoryzomys not only by chromosomal complement, but also in some morphological attributes. The new species is apparently restricted in distribution and endemic of Brazilian Cerrado, occurring only in Rio Tocantins basin.     

Phylogenetic relationships of Mexican minnows of the genus Notropis (Actinopterygii, Cyprinidae)

We conducted phylogenetic analyses based on complete mitochondrial cytochrome b gene sequences among southern and central Mexican cyprinid species, included in the genera Notropis and Hybopsis. In addition 15 northern species of the genera Notropis and Hybopsis were included in the analyses in order to place the Mexican species into a larger phylogenetic framework. The phylogenetic relationships supported the existence of five major clades: (1) including species of the subgenus Alburnops of the genus Notropis plus N. shumardi; (2) species of the subgenus Notropis; (3) species of the genus Hybopsis; (4) species of the N. texanus + N. volucellus species group of the genus Notropis; (5) Mexican endemic species of the genus Notropis plus the genus Yuriria. Previous phylogenetic inferences based on morphological characters resolved the Mexican minnows analysed as N. sallaei, N. calientis, N. boucardi and Y. alta, non‐monophyletic. According to our cytochrome b evidence all Mexican minnows of the genera Notropis and Yuriria formed a monophyletic group with respect to the northern species of the genera Notropis and Hybopsis. Within the Mexican clade, three well‐supported clades were identified: the first included the closely related species N. moralesi and N. boucardi, which occur in three independent drainages of south Mexico; the second consisted of two different lineages, N. imeldae and an undescribed species of Notropis, inhabiting two independent drainages of south Mexico; the third comprised two central Mexican Notropis species (N. calientis and N. sallaei) and the Y. alta populations. Based on this study and pending a more extensive taxonomic revision of the genus Notropis, we adopt the conservative criterion of considering all Notropis species from southern and central Mexico examined, including Y. alta, as belonging to the genus Notropis. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80 , 323–337.     

Phylogenetic relationships in the genus Cheracebus (Callicebinae,Pitheciidae)

Cheracebus is a new genus of New World primate of the family Pitheciidae, subfamily Callicebinae. Until recently, Cheracebus was classified as the torquatus species group of the genus Callicebus. The genus Cheracebus has six species: C. lucifer, C. lugens, C. regulus, C. medemi, C. torquatus, and C. purinus, which are all endemic to the Amazon biome. Before the present study, there had been no conclusive interpretation of the phylogenetic relationships among most of the Cheracebus species. The present study tests the monophyly of the genus and investigates the relationships among the different Cheracebus species, based on DNA sequencing of 16 mitochondrial and nuclear markers. The phylogenetic analyses were based on Maximum Likelihood, Bayesian Inference, and multispecies coalescent approaches. The divergence times and genetic distances between the Cheracebus taxa were also estimated. The analyses confirmed the monophyly of the genus and a well-supported topology, with the following arrangement: ((C. torquatus, C. lugens), (C. lucifer (C. purinus, C. regulus))). A well-differentiated clade was also identified within part of the geographic range of C. lugens, which warrants further investigation to confirm its taxonomic status.     

Phylogenetic relationships within the Archiloa genus complex (Proseriata,Monocelididae)

Of the seven genera which we have recognised within the Archiloa genus complex sensu Karling (1966) the cosmopolitan genus Archilina is the most primitive and is characterised only by plesiomorphic characters, and has to be considered paraphyletic. All other species of the Archiloa genus complex are hypothesized to be derived from Archilina-like ancestors through different evolutionary lineages. One lineage led to the genera Archiloa, Inaloa, Archilopsis and Monocelopsis, taxa found in the Atlantic and the Mediterranean. These genera are monophyletic and their relationships are analyzed. The genera Mesoda (Brazil) and Tajikina (Northern Pacific) can be considered as two other separate lineages. Similarly, within what we now consider as the genus Archilina different lineages can be recognized in different regions.     

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     

Phylogenetic relationships of the newly described species Chondrostoma olisiponensis (Teleostei: Cyprinidae)

Phylogenies were generated using mitochondrial cytochrome b and nuclear ß‐actin gene DNA sequences to infer the phylogenetic relationships of the newly described Chondrostoma olisiponensis. Results indicate that the species is monophyletic with species of the lemmingii‐group in mtDNA phylogenies, while it is monophyletic with species of the arcasii‐group in the nuclear ß‐actin trees. This is in agreement with the morphological resemblance of C. olisiponensis to both species groups. Results from nuclear but not mitochondrial DNA indicate that one population could be currently hybridizing with sympatric Chondrostoma lusitanicum. Based on a relaxed clock calibration of cytochrome b, it is estimated that C. olisiponensis split 12·5–7·9 million years ago (middle–upper Miocene) from its most recent ancestor, which coincides with a period of endorrheism in the Iberian Peninsula.     

Molecular and morphological evidence for a Pleistocene radiation of laminate‐toothed rats (Otomys: Rodentia) across a volcanic archipelago in equatorial Africa

West African Mountains of the Cameroon Volcanic Line harbour two montane‐endemic species of laminated‐toothed rats (Otomys), which represent the most westerly occurrence of the genus. We explore here through mtDNA sequencing and cranial morphometrics the taxonomic status and phylogenetic relationships of O. burtoni (Mt Cameroon) and O. occidentalis (Mts Oku and Gotel). We conclude that both species are valid and can be discriminated by molecular data, as well as quantitative and qualitative cranial characters. From molecular data, O. occidentalis and O. burtoni are closest neighbours (p‐distance = 7.5–8.5%) and weakly associated sister species (suggesting a single West African radiation) and both are sister clades to a well supported clade of central, East and northeast African members of the O. typus s.l. and O. tropicalis s.l. species complexes from mountain ranges comprising the East African ‘Montane Circle’ and Ethiopian Highlands. Re‐evaluation of the evolutionary origins of the allopatric Otomys populations in equatorial Africa is undertaken in light of fossil evidence of a southern African origin of the genus. We can conclude that Otomys reached the Cameroon Volcanic Line via corridors of temperate grasslands during the Late Pliocene. Our data support the hypothesis that, following major peripatric speciation events at around 2.3 to 2.03 Ma (from East Africa into West and North Africa respectively), further speciation occurred across neighbouring mountain ranges in West, Central‐East and North‐East Africa. Estimated molecular dates of speciation events in Otomys reveal close congruence with well‐constrained geochronological estimates, pertinently the uplift of the Albertine Rift in the Early Pleistocene. These regional analyses reveal how peripatric speciation events established narrow‐range endemics of Otomys on principal stratovolcanoes across the East African plateau and Cameroon. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 320–344.     

Phylogenetic relationships of Moxostoma and Scartomyzon (Catostomidae) based on mitochondrial cytochrome b sequence data

A recent phylogenetic study based on morphological, biochemical and early life history characters resurrected the genus Scartomyzon (jumprock suckers, c . eight−10 species) from Moxostoma (redhorse suckers, c . 10–11 species) and advanced the understanding of relationships among species in these two genera, and the genealogical affinities of these genera with other evolutionary lineages within the tribe Moxostomatini in the subfamily Catostominae. To further examine phylogenetic relationships among moxostomatin suckers, the complete mitochondrial (mt) cytochrome b gene was sequenced from all species within this tribe and representative outgroup taxa from the Catostomini and other catostomid subfamilies. Phylogenetic analysis of gene sequences yielded two monophyletic clades within Catostominae: Catostomus + Deltistes + Xyrauchen + Erimyzon + Minytrema and Moxostoma + Scartomyzon + Hypentelium + Thoburnia . Within the Moxostomatini, Thoburnia was either unresolved or polyphyletic; Thoburnia atripinnis was sister to a monophyletic Hypentelium . In turn, this clade was sister to a monophyletic clade containing Scartomyzon and Moxostoma . Scartomyzon was never resolved as monophyletic, but was always recovered as a polyphyletic group embedded within Moxostoma , rendering the latter genus paraphyletic if ' Scartomyzon ' continues to be recognized. Relationships among lineages within the Moxostoma and' Scartomyzon 'clade were resolved as a polytomy. To better reflect phylogenetic relationships resolved in this analysis, the following changes to the classification of the tribe Moxostomatini are proposed: subsumption of' Scartomyzon 'into Moxostoma ; restriction of the tribe Moxostomatini to Moxostoma ; resurrect the tribe Erimyzonini, containing Erimyzon and Minytrema , classified as incertae sedis within Catostominae; retain the tribe Thoburniini.     

Glaciation effects on the phylogeographic structure of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in the southern Andes

The long-tailed pygmy rice rat Oligoryzomys longicaudatus (Sigmodontinae), the major reservoir of Hantavirus in Chile and Patagonian Argentina, is widely distributed in the Mediterranean, Temperate and Patagonian Forests of Chile, as well as in adjacent areas in southern Argentina. We used molecular data to evaluate the effects of the last glacial event on the phylogeographic structure of this species. We examined if historical Pleistocene events had affected genetic variation and spatial distribution of this species along its distributional range. We sampled 223 individuals representing 47 localities along the species range, and sequenced the hypervariable domain I of the mtDNA control region. Aligned sequences were analyzed using haplotype network, bayesian population structure and demographic analyses. Analysis of population structure and the haplotype network inferred three genetic clusters along the distribution of O. longicaudatus that mostly agreed with the three major ecogeographic regions in Chile: Mediterranean, Temperate Forests and Patagonian Forests. Bayesian Skyline Plots showed constant population sizes through time in all three clusters followed by an increase after and during the Last Glacial Maximum (LGM; between 26,000-13,000 years ago). Neutrality tests and the "g" parameter also suggest that populations of O. longicaudatus experienced demographic expansion across the species entire range. Past climate shifts have influenced population structure and lineage variation of O. longicaudatus. This species remained in refugia areas during Pleistocene times in southern Temperate Forests (and adjacent areas in Patagonia). From these refugia, O. longicaudatus experienced demographic expansions into Patagonian Forests and central Mediterranean Chile using glacial retreats.     

Phylogenetic relationships of Eurasian and American cyprinids using cytochrome b sequences

Neighbour-joining and parsimony analyses identified five lineages of cyprinids: (1) European leuciscins (including Notemigonus )+North American phoxinins (including Phoxinus phoxinus ); (2) European gobionins+Pseudorasbora ; (3) primarily Asian groups [cultrins+acheilognathins+ gobionins (excluding Abbotina )+xenocyprinins]; (4) Abbottina+Sinocyclocheilus+Acrossocheilus ; (5) cyprinins [excluding Sinocyclocheilus and Acrossocheilus ]+barbins+labeonins. Relationships among these lineages and the enigmatic taxa Rhodeus were not well-resolved. Tests of monophyly of subfamilies and previously proposed relationships were examined by constraining cytochrome b sequences data to fit previous hypotheses. The analysis of constrained trees indicated that sequence data were not consistent with most previously proposed relationships. Inconsistency was largely attributable to Asian taxa, such as Xenocypris and Xenocyprioides . Improved understanding of historical and taxonomic relationships in Cyprinidae will require further morphological and molecular studies on Asian cyprinids and taxa representative of the diversity found in Africa.