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.     

Molecular systematics and biogeography of the Neotropical monkey genus,Alouatta

We take advantage of the broad distribution of howler monkeys from Mexico to Argentina to provide a historical biogeographical analysis on a regional scale that encompasses the entire Neotropics. The phylogenetic relationships among 9 of the 10 recognized Alouatta species were inferred using three mitochondrial and two nuclear genes. The nuclear gene regions provided no phylogenetic resolution among howler monkey species, and were characterized by very low levels of sequence divergence between Alouatta and the Ateles outgroup. The mtDNA genes, on the other hand, produced a well-resolved phylogeny, which indicated that the earliest split among howler monkeys separated cis- and trans-Andean clades. Eight monophyletic mtDNA haplotype clades were identified, representing six named species in South America, including Alouatta seniculus, Alouatta sara, Alouatta macconelli, Alouatta caraya, Alouatta belzebul, and Alouatta guariba, and two in Mesoamerica, Alouatta pigra and Alouatta palliata. Molecular clock-based estimates of branching times indicated that contemporary howler monkey species originated in the late Miocene and Pliocene, not the Pleistocene. The causes of Alouatta diversification were more difficult to pin down, although we posit that the initial cis-, trans-Andean split in the genus was caused by the late Miocene completion of the northern Andes. Riverine barriers to dispersal and putative forest refuges can neither be discounted nor distinguished as causes of speciation in many cases, and one, the other or both have likely played a role in the diversification of South American howler monkeys. Finally, we estimated the separation of Mesoamerican A. pigra and A. palliata at 3Ma, which corresponds to the completion date of the Panama Isthmus promoting a role for this earth history event in the speciation of Central American howler monkeys.     

Molecular systematics and biogeography of the western Mediterranean stonefly genus Tyrrhenoleuctra (Insecta, Plecoptera)

The stonefly genus Tyrrhenoleuctra includes species living in western Mediterranean temporary freshwater streams, sometimes also at sea level, a very unusual habitat for most Plecoptera. Traditional morphological approaches proved unsuccessful in drawing both taxonomic and phylogenetic patterns, thus hampering discussion of biogeographical patterns for this interesting group. We aimed at: (a) assessing the taxonomic status of populations of Tyrrhenoleuctra covering the geographic range of the genus; (b) studying the phylogenetic relationships among the recognized species; and (c) describing biogeographic patterns. We used phylogenetic analyses to infer the phylogenetic history of this group of stoneflies based on a combined data set of 1666 bp including fragments of the 12S ribosomal (12S) and cytochrome oxidase I (CO‐I) mtDNA genes, with maximum likelihood and Bayesian methods. Two main clades have been identified: a Sardo‐Corsican one, including Tyrrhenoleuctra zavattarii, and an Ibero‐Maghrebian one including four lineages of unkown taxonomic rank from the Balearic Islands (Maiorca), from northern Africa (Ceuta) and southernmost Spain (Algeciras), and a complex preliminarily referred herein to T. minuta (Klapálek, 1901), which includes two lineages, one from Cordoba, and one from Sierra de Grazalema (El Cerro) and Portugal (Tellhares) respectively. Dating the nodes by fixing the split of the Ibero‐Maghrebian clade from the Sardo‐Corsican one at 29 million years ago (Mya), yielded dates referring to the major geological events in the Mediterranean basin. Estimated molecular evolutionary rates ranged from 0.02–0.09% per million years (my) in the T. zavattarii lineages, to 0.2–0.7% per MY in the Ibero‐Maghrebian clade. The phylogenetic pattern emerged from the present study is congruent with the known paleo‐history of the western Mediterranean basin, with the divergence of the two main Tyrrhenoleuctra lineages corresponding to the split of the Sardo‐Corsican microplate from the Iberian block. Vicariance events have characterized the history of this stonefly group along its entire biogeographical history. Surprisingly low evolutionary rates, previously supposed by Fochetti (1991, 1994) and Fochetti et al. (2004) based on nuclear markers (allozymes), have been herein found also in mitochondrial markers.     

Molecular systematics and biogeography of theCardamine pratensis complex (Brassicaceae)

Representatives of theC. pratensis complex were analysed for allozymes, ITS, non-coding cpDNA, and RAPDs to elucidate phylogenetic relationships and the historical biogeography of this species group. Our concepts differ in some important aspects from current ideas. Two diploid species from southeastern Europe form the Basal Group of the complex. A diploid from the Iberian Peninsula represents another old lineage. The phylogenetically younger Derived Group comprises diploid taxa and all known polyploid taxa. The two old lineages represent pleistocene relicts which were not involved in the formation of the Derived Group. All polyploids evolved in postglacial time from diploids of the Derived Group which may have survived the glaciations in refugia centered around and within the Alps. The arctic-circumpolarC. nymanii is of young age and migrated to Scandinavia in postglacial times from south to north.     

Historical biogeography and molecular systematics of the Indo-Pacific genus Dascyllus (Teleostei: Pomacentridae)

The phylogeographical and systematic relationships among species in the tropical marine fish genus Dascyllus were inferred using mitochondrial DNA (mtDNA) sequence data. Although our results were generally consistent with previously published phylogenies based on both morphological and mitochondrial data, our broad taxonomic and geographical sampling design revealed novel insights into the phylogenetic history of Dascyllus that had escaped previous notice. These results include: (a) the polyphyletic nature of D. reticulatus mtDNAs, representing two divergent and geographically separated lineages, one shared with D. flavicaudus and the second forming the sister lineage of D. carneus; (b) the paraphyly of D. trimaculatus relative to the closely related D. abisella; and (c) phylogeographical structure within the widespread taxa D. aruanus and D. trimaculatus. Application of a molecular clock permits us to posit a causative role for tectonic and oceanic changes regarding some Dascyllus speciation events. Finally, we mapped body size and the presence or absence of protogynous sex change on the mtDNA tree, and tested published hypotheses regarding determinants of the evolution of mating system and protogyny in the genus. Our data rejected a model based on body size but not one based on phylogenetic inertia. The ability to change sex arose once in the ancestor to the entire genus, and was lost once in the ancestor of the D. trimaculatus complex. For taxa that are as geographically widespread as many Indo-Pacific genera, this study highlights the importance of adequate geographical sampling when inferring patterns of species diversification and life history evolution.     

Molecular systematics, biogeography and population structure of neotropical freshwater needlefishes of the genus Potamorrhaphis

Phylogenetic relationships of populations and species within Potamorrhaphis, a genus of freshwater South American needlefishes, were assessed using mitochondrial cytochrome b sequences. Samples were obtained from eight widely distributed localities in the Amazon and Orinoco rivers, and represented all three currently recognized species of Potamorrhaphis. The phylogeny of haplotypes corresponded imperfectly to current morphological species identities: haplotypes from P. guianensis, the most widespread species, did not make up a monophyletic clade. Geography played a strong role in structuring genetic variation: no haplotypes were shared between any localities, indicating restricted gene flow. Possible causes of this pattern include limited dispersal and the effects of current and past geographical barriers. The haplotype phylogeny also showed a complex relationship between fishes from different river basins. Based on the geographical distribution of clades, we hypothesize a connection between the middle Orinoco and Amazon via rivers of the Guianas. More ancient divergence events may have resulted from Miocene alterations of river drainage patterns. We also present limited data for two other Neotropical freshwater needlefish genera: Belonion and Pseudotylosurus. Pseudotylosurus showed evidence of substantial gene flow between distant localities, indicating ecological differences from Potamorrhaphis.     

Molecular systematics of the genus Artibeus (Chiroptera: Phyllostomidae)

A molecular phylogeny of the genus Artibeus using 19 of the 20 recognized species, many with samples from a broad geographic range, is presented. The analysis shows a clear distinction between the two subgenera (or genera), the 'large'Artibeus and the 'small'Dermanura, in both mitochondrial and nuclear genes. The placement and status of A. concolor remains inconclusive and is presented as the third subgenus Koopmania. The phylogenies and divergence time estimates show a marked influence of the Andes in the formation of the subgenera and the main lineages inside each subgenus. Nuclear genes showed a highly incomplete lineage sorting among species inside subgenera Artibeus and Dermanura. Indeed, shared alleles were also found between Artibeus and Koopmania, which are presumed to have split apart during the Miocene, showing that great care should be taken in using these markers. Cytochrome-b gene divergences and monophyly analyses suggest that A. lituratus and A. intermedius are indeed conspecifics. These analyses also suggested the existence of at least four 'new' species revealing a significant cryptic diversity inside the genus.     

Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae)

Background and Aims

Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented.

Methods

A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications.

Key Results

The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions.

Conclusions

This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris.     

Molecular systematics of the genus Allodontichthys (Cyprinodontiformes: Goodeidae)

Phylogenetic analyses of cytochrome c oxidasesubunit I (627bp) and mitochondrial controlregion (338bp aligned) sequences for all knownspecies of Allodontichthys wereperformed. Allodontichthys was recoveredas monophyletic, and A. hubbsi wassupported as the most primitive member of thegenus in all analyses. Combined-data analysessuggest that A. polylepis is sister to aclade comprising A. tamazulae and A. zonistius; however, a strict consensus of COIand control region cladograms results in acollapse of this node. The two species thatare broadly sympatric, A. hubbsi and A. tamazulae, are not sister taxa.Allodontichthys was found the sistergroup of a clade including Ilyodon andXenotaenia. These three genera are theonly goodeids to occupy high-gradient riversystems. Ilyodon and Allodontichthys share similar distributions;however, Allodontichthys exhibits greaterthan an order of magnitude more geneticvariation in COI than Ilyodon incomparisons of individuals from the samelocalities in the Ameca and Armeria drainagesystems. This is interpreted to mean Allodontichthys arrived in some westerndrainages significantly before Ilyodon.The Rio Coahuayana appears to be the center oforigin of the genus Allodontichthys. This river basin contains the most primitivemember of the genus, and appears to haveconnected with the Mesa Central, the center of endemism of the Goodeidae. A calibrated rateof molecular change in COI reveals Allodontichthys began diverging approximately6.2 million years ago (mya). Remainingspeciation in the group appears to haveoccurred about 2.7 to 3.3 mya. The hypothesisthat a hard polytomy comprising A. zonistius, A. polylepis, and A. tamazulae could be explained by speciation ofA. polylepis and A. tamazulae fromdifferent A. zonistius ancestors ispresented. Stream capture is evident but notfrequent in the history of Allodontichthys, and speciation does notclearly correlate with documented geologicactivity of the Mexican Transvolcanic Belt.     

Molecular phylogeny of the Forcipulatacea (Asteroidea: Echinodermata): systematics and biogeography

We present a comprehensively sampled three‐gene phylogeny of the monophyletic Forcipulatacea, one of three major lineages within the crown‐group Asteroidea. We present substantially more Southern Hemisphere and deep‐sea taxa than were sampled in previous molecular studies of this group. Morphologically distinct groups, such as the Brisingida and the Zoroasteridae, are upheld as monophyletic. Brisingida is supported as the derived sister group to the Asteriidae (restricted), rather than as a basal taxon. The Asteriidae is paraphyletic, and is broken up into the Stichasteridae and four primary asteriid clades: (1) a highly diverse boreal clade, containing members from the Arctic and sub‐Arctic in the Northern Hemisphere; (2) the genus Sclerasterias; (3) and (4) two sister clades that contain asteriids from the Antarctic and pantropical regions. The Stichasteridae, which was regarded as a synonym of the Asteriidae, is resurrected by our results, and represents the most diverse Southern Hemisphere forcipulatacean clade (although two deep‐sea stichasterid genera occur in the Northern Hemisphere). The Labidiasteridae is artificial, and should be synonymized into the Heliasteridae. The Pedicellasteridae is paraphyletic, with three separate clades containing pedicellasterid taxa emerging among the basal Forcipulatacea. Fossils and timing estimates from species‐level phylogeographic studies are consistent with prior phylogenetic hypotheses for the Forcipulatacea, suggesting diversification of basal taxa in the early Mesozoic, with some evidence for more widely distributed ranges from Cretacous taxa. Our analysis suggests a hypothesis of an older fauna present in the Antarctic during the Eocene, which was succeeded by a modern Antarctic fauna that is represented by the recently derived Antarctic Asteriidae and other forcipulatacean lineages. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 646–660.     

Molecular systematics and historical biogeography of the Black-browed Barbet species complex (Megalaima oorti)

Although Southeast Asia is a global biodiversity hotspot, the tempo and mode of avian diversification there has not been well studied. We investigated the history of the diversification of an endemic Asian tropical bird, the Black-browed Barbet Megalaima oorti , by reconstructing its intraspecific molecular phylogeny with mitochondrial cytochrome- b gene sequences. Our molecular phylogeny suggests that the five subspecies of this montane barbet comprise four deeply divergent clades with strong geographical associations: M. o. oorti in the Malay Peninsula and Sumatra, M. o. annamensis in Vietnam, M. o. nuchalis in Taiwan and M. o. faber / M. o. sini in Hainan and the southeastern Chinese mainland, respectively. Climate changes from the mid-Pliocene to the Pleistocene may have influenced their diversification through repeated contraction and expansion of Asian tropical forest. Moreover, our data indicate that the Black-browed Barbet complex is not monophyletic: M. asiatica is embedded in our phylogeny as the sister taxon to M. o. annamensis . The present taxonomic treatment has combined evolutionarily distinct taxa into a single paraphyletic species. Based on our molecular data and previously published plumage characters, we suggest a revision of traditional M. oorti into four monophyletic species: M. oorti , M. nuchalis , M. annamensis and M. faber .     

Molecular systematics of the genus Neotoma

DNA sequences from the mitochondrial DNA cytochrome-b gene were used to infer the systematic relationships of 13 species of wood rats (genus Neotoma). Parsimony, likelihood, and neighbor-joining analyses produced similar topologies in most cases and produced six systematic conclusions. First, results of previous studies were supported in the recognition of N. floridana magister as distinct species (N. magister). Second, evidence was provided for the recognition of cryptic species within N. albigula (N. albigula and N. leucodon) and N. mexicana (N. mexicana, N. isthmica, and N. picta). Third, the subgenus Neotoma is composed of four species groups (floridana, lepida, mexicana, and micropus). Fourth, support was provided for placement of N. stephensi within the lepida species group. Fifth, support was provided for the recognition of Hodomys as a separate genus, sister to Xenomys. Sixth, support for the elevation of the subgenus Teonoma to generic status is discussed.     

Molecular phylogeny, biogeography, and systematics of Dicerandra (Lamiaceae), a genus endemic to the southeastern United States

Dicerandra, an endemic mint of the southeastern United States, comprises nine species, all of which are threatened or endangered and restricted to sandhill vegetation and a mosaic of scrub habitats. Molecular phylogenetic analyses of Dicerandra based on data from the nuclear and plastid genomes for all 13 taxa of the genus, identified two strongly supported clades, corresponding to the four annual and to the five perennial species of Dicerandra. However, the nuclear and plastid trees were incongruent in their placement of two perennial taxa, D. cornutissima and D. immaculata var. savannarum, perhaps due to ancient hybridization or to lineage sorting. Based on these analyses, the widespread D. linearifolia is not monophyletic, with populations of D. linearifolia var. linearifolia falling into either western or eastern clades. The western clade, comprising populations of D. linearifolia var. linearifolia and var. robustior, occurs in an area drained by rivers flowing toward the Gulf of Mexico, whereas the eastern clade, comprising populations of D. linearifolia var. linearifolia, D. densiflora, D. odoratissima, and D. radfordiana (i.e., all the annual species), occupies a region drained by rivers flowing to the Atlantic Ocean. Although this pattern of genetic differentiation between populations from these two river drainages has been documented in several animal species, it has not previously been reported for plants. A revised subgeneric classification is presented to reflect the annual and perennial clades.     

Molecular systematics and global phylogeography of angel sharks (genus Squatina)

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe–North Africa–Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events.     

Molecular phylogenetics,character evolution and systematics of the genus Micranthes (Saxifragaceae)

With c. 85 species, the genus Micranthes is among the larger genera of the Saxifragaceae. It is only distantly related to the morphologically similar genus Saxifraga, in which it has frequently been included as Saxifraga section Micranthes. To study the molecular evolution of Micranthes, we analysed nuclear ribosomal (internal transcribed spacer, ITS) and plastid (trnL–trnF) DNA sequences in a comprehensive set of taxa comprising c. 75% of the species. The molecular phylogenetic tree from the combined dataset revealed eight well‐supported clades of Micranthes. These clades agree in part with previously acknowledged subsections or series of Saxifraga section Micranthes. As these eight groups can also be delineated morphologically, we suggest that they should be recognized as sections of Micranthes. New relationships were also detected for some species and species groups, e.g. section Davuricae sister to sections Intermediae and Merkianae, and M. micranthidifolia as a member of section Micranthes. Species proposed to be excluded from the genus Micranthes for morphological reasons were resolved in the molecular tree in Saxifraga. Many morphological characters surveyed were homoplasious to varying extents. Micromorphological characters support comparatively well the clades in the phylogenetic tree. An updated nomenclature and a taxonomic conspectus of sections and species of Micranthes are provided. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 47–66.     

Molecular systematics and evolutionary history of the genus Carabus (Col. Carabidae)

Despite the number of evolutionary, ecological and conservation studies that are conducted on Carabus, the global evolutionary history of the genus remains poorly understood. Here, we analysed 7.5 kilobases of DNA sequence data (six mitochondrial and four nuclear genes) from a worldwide sample of 45% of the known subgenera (99 species and 14 subspecies). We compared the nuclear and mitochondrial phylogenies obtained from Maximum likelihood and Bayesian analyses through topological tests of congruence and dating analyses. Our results mostly corroborate the monophyly of the morphological subgroups of Carabus. However, current morphological and molecular data appear unable to accurately infer the deep branchings within the genus. We show that Carabus originated ca. 16.7-25.1Ma, approximately 25Myr later than previously estimated. Major groups of Carabus are subdivided into clades that diverged from each other in a relatively short period of time around 10Ma (6.6-14.8). This time frame suggests that the present-day distribution of Carabus subgroups may be explained by isolation resulting from Eurasian forest fragmentation brought on by Miocene climate changes and by mountain orogenesis. Finally, we highlight several conflicts between mitochondrial and nuclear topologies that may be explained by mitochondrial introgression.     

Molecular systematics of the Middle American genus Hypopachus (Anura: Microhylidae)

We present the first phylogenetic study on the widespread Middle American microhylid frog genus Hypopachus. Partial sequences of mitochondrial (12S and 16S ribosomal RNA) and nuclear (rhodopsin) genes (1275 bp total) were analyzed from 43 samples of Hypopachus, three currently recognized species of Gastrophryne, and seven arthroleptid, brevicipitid and microhylid outgroup taxa. Maximum parsimony (PAUP), maximum likelihood (RAxML) and Bayesian inference (MrBayes) optimality criteria were used for phylogenetic analyses, and BEAST was used to estimate divergence dates of major clades. Population-level analyses were conducted with the programs NETWORK and Arlequin. Results confirm the placement of Hypopachus and Gastrophryne as sister taxa, but the latter genus was strongly supported as paraphyletic. The African phrynomerine genus Phrynomantis was recovered as the sister taxon to a monophyletic Chiasmocleis, rendering our well-supported clade of gastrophrynines paraphyletic. Hypopachus barberi was supported as a disjunctly distributed highland species, and we recovered a basal split in lowland populations of Hypopachus variolosus from the Pacific versant of Mexico and elsewhere in the Mesoamerican lowlands. Dating analyses from BEAST estimate speciation within the genus Hypopachus occurred in the late Miocene/early Pliocene for most clades. Previous studies have not found bioacoustic or morphological differences among these lowland clades, and our molecular data support the continued recognition of two species in the genus Hypopachus.     

Molecular systematics, phylogeny and biogeography of roaches (Rutilus, Teleostei, Cyprinidae)

In this study we used sequence data from the entire mtDNA cytochrome b gene to reconstruct patterns and times of diversification in the roach genus Rutilus. The genus is present with numerous endemic species in the Eastern peri-Mediterranean area and with a few widespread species in Central Europe. Our phylogenetic results do not support the subdivision into two subgenera proposed on morphological grounds. Within R. pigus and R. rutilus we identify highly divergent and allopatric mitochondrial lineages. The deeper splits in the genus phylogeny date back to the middle Miocene; the main diversification took place at the Miocene-Pliocene boundary.