Mastigopterus imperator Smith and Radcliffe, 1913, a senior synonym of M. praetor Smith and Radcliffe, 1913 (Ophidiidae, Ophidiiformes)

 A rare deep-sea ophidiid genus Mastigopterus known to contain two species, M. imperator Smith and Radcliffe, 1913 and M. praetor Smith and Radcliffe, 1913, was reviewed on the basis of six specimens including the holotypes of both species. Dorsal and anal fin ray counts and the size of cephalic sensory pores previously thought to be diagnostic characteristics to discriminate the two species did not suggest the presence of two forms, the large (M. imperator) and the small species (M. praetor), in the genus. Apparently the genus is represented by a single species, M. imperator, known from off Madagascar, the East and South China Seas and Papua New Guinea. Received: September 7, 1999 / Revised: July 9, 2001 / Accepted: November 13, 2001     

Contributions to the Cladocera fauna from Papua New Guinea

Twenty-eight taxa of the Cladocera are identified in collections from Papua New Guinea, 17 being new records for New Guinea, bringing the total number of Cladocera taxa reported for this region to 39. Most of the taxa are circumtropical. One species (Sarsilatona papuana) is endemic to Papua New Guinea and northern Australia. The species list includes two species that are normally listed as Holarctic:Alonella nana andAlona rustica. Widespread genera such asDaphnia, Pleuroxus, Disparalona, Acroperus were strikingly absent from the Papua New Guinean material.     

Phylogeography of the pademelons (Marsupialia: Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio‐Pleistocene

Aim Alternative hypotheses concerning genetic structuring of the widespread endemic New Guinean forest pademelons (Thylogale) based on current taxonomy and zoogeography (northern, southern and montane species groupings) and preliminary genetic findings (western and eastern regional groupings) are investigated using mitochondrial sequence data. We examine the relationship between the observed phylogeographical structure and known or inferred geological and historical environmental change during the late Tertiary and Quaternary. Location New Guinea and associated islands. Methods We used primarily museum specimen collections to sample representatives from Thylogale populations across New Guinea and three associated islands. Mitochondrial cytochrome b and control region sequence data were used to construct phylogenies and estimate the timing of population divergence. Results Phylogenetic analyses indicated subdivision of pademelons into ‘eastern’ and ‘western’ regional clades. This was largely due to the genetic distinctiveness of north‐eastern and eastern peninsula populations, as the ‘western’ clade included samples from the northern, southern and central regions of New Guinea. Two tested island groups were closely related to populations north of the Central Cordillera; low genetic differentiation of pademelon populations between north‐eastern New Guinea and islands of the Bismarck Archipelago is consistent with late Pleistocene human‐mediated translocations, while the Aru Islands population showed divergence consistent with cessation of gene flow in the mid Pleistocene. There was relatively limited genetic divergence between currently geographically isolated populations in subalpine and nearby mid‐montane or lowland regions. Main conclusions Phylogeographical structuring does not conform to zoogeographical expectations of a north/south division across the cordillera, nor to current species designations, for this generalist forest species complex. Instead, the observed genetic structuring of Thylogale populations has probably been influenced by geological changes and Pleistocene climatic changes, in particular the recent uplift of the north‐eastern Huon Peninsula and the lowering of tree lines during glacial periods. Low sea levels during glacial maxima also allowed gene flow between the continental Aru Island group and New Guinea. More work is needed, particularly multi‐taxon comparative studies, to further develop and test phylogeographical hypotheses in New Guinea.     

Australasian sky islands act as a diversity pump facilitating peripheral speciation and complex reversal from narrow endemic to widespread ecological supertramp

The Australasian archipelago is biologically extremely diverse as a result of a highly puzzling geological and biological evolution. Unveiling the underlying mechanisms has never been more attainable as molecular phylogenetic and geological methods improve, and has become a research priority considering increasing human‐mediated loss of biodiversity. However, studies of finer scaled evolutionary patterns remain rare particularly for megadiverse Melanesian biota. While oceanic islands have received some attention in the region, likewise insular mountain blocks that serve as species pumps remain understudied, even though Australasia, for example, features some of the most spectacular tropical alpine habitats in the World. Here, we sequenced almost 2 kb of mitochondrial DNA from the widespread diving beetle Rhantus suturalis from across Australasia and the Indomalayan Archipelago, including remote New Guinean highlands. Based on expert taxonomy with a multigene phylogenetic backbone study, and combining molecular phylogenetics, phylogeography, divergence time estimation, and historical demography, we recover comparably low geographic signal, but complex phylogenetic relationships and population structure within R. suturalis. Four narrowly endemic New Guinea highland species are subordinated and two populations (New Guinea, New Zealand) seem to constitute cases of ongoing speciation. We reveal repeated colonization of remote mountain chains where haplotypes out of a core clade of very widespread haplotypes syntopically might occur with well‐isolated ones. These results are corroborated by a Pleistocene origin approximately 2.4 Ma ago, followed by a sudden demographic expansion 600,000 years ago that may have been initiated through climatic adaptations. This study is a snapshot of the early stages of lineage diversification by peripatric speciation in Australasia, and supports New Guinea sky islands as cradles of evolution, in line with geological evidence suggesting very recent origin of high altitudes in the region.     

Phylogenetic relationships and divergence date estimates among Australo‐Papuan mosaic‐tailed rats from the Uromys division (Rodentia: Muridae)

Bryant, L. M., Donnellan, S. C., Hurwood, D. A. & Fuller, S. J. (2011). Phylogenetic relationships and divergence date estimates among Australo‐Papuan mosaic‐tailed rats from the Uromys division (Rodentia: Muridae). —Zoologica Scripta, 40, 433–447. We inferred phylogenetic relationships and divergence date estimates among four genera of mosaic‐tailed rats from the Uromys division in Australia, New Guinea and the Solomon Islands from both mitochondrial (16S rRNA) and nuclear (AP5 and DHFR introns) nucleotide sequence data. Phylogenetic analysis of our combined data shows that Melomys species from Australia and New Guinea are monophyletic to the exclusion of Paramelomys, which last shared a common ancestor with other members of the Uromys division approximately 3 MYA. However, Melomys was found to be paraphyletic with respect to the Solomon Islands endemic Solomys, suggesting the taxonomic distinction of the latter may need revision. The radiation of this group was estimated to have occurred between 2.1 MYA and 900 000 years ago. A currently undescribed taxon, species nova, which is apparently morphologically indistinguishable from sympatric M. cervinipes, was found to be a highly distinctive lineage and was not monophyletic with Melomys from Australia or New Guinea. Australian Uromys share a sister group relationship with sp. n. and the Melomys/Solomys clade. Australian Melomys were not monophyletic with respect to New Guinean Melomys. The New Guinean M. lutillus and Australian M. burtoni appear to be conspecific, supporting a previous suggestion that M. burtoni has an extralimital distribution encompassing New Guinea as M. lutillus. This also suggests sustained contact between these taxa, most likely enabled through historical landbridges that linked the two landmasses during periods of lower sea level. Melomys rubicola, found only on Bramble Cay, 50 km south of New Guinea, is more closely related to Australian Melomys, particularly M. capensis, than to any of the New Guinean species. Results suggest that M. rubicola and M. capensis last shared a common ancestor in the early Pleistocene, a time when land bridges existed connecting Bramble Cay to Cape York. Finally, polyphyly within M. cervinipes was also detected, corresponding to reciprocally monophyletic northern and southern clades. The northern M. cervinipes clade diverged from the M. capensis/rubicola clade approximately 1.2 MYA, with this split possibly resulting from isolation across the Normanby gap in far north Queensland.     

Fifteen into Three Does Go: Morphology,Genetics and Genitalia Confirm Taxonomic Inflation of New Zealand Beetles (Chrysomelidae: Eucolaspis)

Eucolaspis Sharp 1886 is a New Zealand native leaf beetle genus (Coleoptera: Chrysomelidae: Eumolpinae) with poorly described species and a complex taxonomy. Many economically important fruit crops are severely damaged by these beetles. Uncertain species taxonomy of Eucolaspis is leaving any biological research, as well as pest management, tenuous. We used morphometrics, mitochondrial DNA and male genitalia to study phylogenetic and geographic diversity of Eucolaspis in New Zealand. Freshly collected beetles from several locations across their distribution range, as well as identified voucher specimens from major museum collections were examined to test the current classification. We also considered phylogenetic relationships among New Zealand and global Eumolpinae (Coleoptera: Chyrosomelidae). We demonstrate that most of the morphological information used previously to define New Zealand Eucolaspis species is insufficient. At the same time, we show that a combination of morphological and genetic evidence supports the existence of just 3 mainland Eucolaspis lineages (putative species), and not 5 or 15, as previously reported. In addition, there may be another closely related lineage (putative species) on an offshore location (Three Kings Islands, NZ). The cladistic structure among the lineages, conferred through mitochondrial DNA data, was well supported by differences in male genitalia. We found that only a single species (lineage) infests fruit orchards in Hawke’s Bay region of New Zealand. Species-host plant associations vary among different regions.     

Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (<Emphasis Type="Italic">Sericornis</Emphasis>) and mouse-warblers (<Emphasis Type="Italic">Crateroscelis</Emphasis>), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae)

Understanding how the complex geotectonic and climatic history of the Australo-Papuan region has promoted the ecological and evolutionary diversification of its avifauna remains a challenge. Outstanding questions relate to the nature and timing of biogeographical connections between Australia and the emerging island of New Guinea and the mechanisms by which distinctive altitudinal replacement sequences have evolved amongst congeneric species in montane New Guinea. Here, we combine analyses of phylogenetic and eco-morphological data to investigate ecological and evolutionary patterns of diversification in the largely mesic-adapted Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis). We find evidence of ecological convergence and present a revised taxonomic and systematic treatment of the subfamily integrating information from new (ND2) and existing molecular phylogenetic reconstructions. Biogeographical connections indicate at least three phases of faunal interchange between Australia and New Guinea commencing in the mid to late Miocene. We also find little support for the proposed time dependency of ecological sorting mechanisms linked to divergence in foraging niche amongst altitudinal replacements. Instead, physiological adaptations to hypoxia and increased thermal efficiency at higher altitudes may better account for observed patterns of diversification in montane New Guinea. Indirect support for this hypothesis is derived from molecular clock calibrations that indicate a pulse of diversification across the Miocene-Pliocene boundary coincident with a phase of rapid mountain uplift. Simple ecological and climatic models appear inadequate for explaining observed patterns and mechanisms of diversification in the New Guinean montane avifauna. Further insights will require multidisciplinary research integrating geotectonic, palaeoclimatic, genetic, ecological and physiological approaches.     

<Emphasis Type="Italic">Atactorhynchus duranguensis</Emphasis> n. sp. (Acanthocephala: Atactorhynchinae) from <Emphasis Type="Italic">Cyprinodon meeki</Emphasis> (Pisces: Cyprinodontidae) near Durango,Mexico

Atactorhynchus duranguensisn. sp. (Acanthocephala: Atactorhynchinae) is described from the intestine of Cyprinodon meeki Miller, an endemic freshwater fish from a far-inland locality of Mexico. Diagnostic features include: body small, stout, ventrally curved; small cylindrical proboscis armed with 16 alternating vertical rows of four or five hooks; anterior two or three hooks conspicuous, stout and larger than other hooks, and have large, rod-shaped roots with a markedly and abruptly enlarged base; three posterior hooks of each row are smaller and rootless; single-walled proboscis receptacle; lemnisci equal in length, elongate and robust; and cement gland syncytial, larger than testis. The new species is smaller than A. verecundus Chandler, 1935, the only previously described species in the genus. The shape of the proboscis of the new species is strikingly different from that of A. verecundus, which is widest at the apex. Likewise, the greatest width of the trunk of the new species is in about the middle, differing from that of A. verecundus where the trunk is widest posteriorly. The new species also can be distinguished from A. verecundus because of its much smaller hook lengths and slightly smaller proboscis. In addition, the proportion of large apical proboscis hooks in relation to the small basal hooks is different: the basal hooks of A. verecundus are about half the size of the anterior hooks and but only about a quarter of the size in A. duranguensis. Unlike A. verecundus, the base of the roots are markedly and abruptly enlarged in the new species. Finally, the eggs of the new species are smaller (23–27 × 8–10 m) than those of A. verecundus (27–30 × 12–13 m).     

A revision of Ptychopyxis (Euphorbiaceae) in southeast Asia

Ptychopyxis is a genus comprised of 11 species. Nine are found in southeast Asia mainland and west Malesia and two species are endemic to New Guinea. One of the endemic New Guinean species is newly described here, viz. P. esdras Stoops sp. nov.     

Species limits in the genus Bleda Bonaparte, 1857 (Aves,Pycnonotidae)

African forest bulbuls of the genus Bleda are usually placed into three separate species: B. syndactyla and B. eximia distributed both in Upper and Lower Guinea forest blocks, and B. canicapilla restricted to the Upper Guinean one. Acoustic data lead to question traditional morphologically-based species limits in this genus. Colouration patterns and measurements, particularly bill shape and length, wing and tail lengths, are reconsidered for all taxa. Multivariate (discriminant functions) analyses lead to separate nominate B. eximia as an Upper Guinean species distinct from Lower Guinean B. notata. Furthermore B. eximia appears closer to B. syndactyla than to the other two species. Acoustically, by the physical traits of their calls and songs as well as the behaviour associated with their production, B. eximia and B. syndactyla are very close and quite different from B. canicapilla and B. notata which constitute another pair of very close species. Obviously, in the frame of the biological species concept, the four taxa branched in two groups from a common ancestor, B. eximia and B. syndactyla represent a species-pair whereas B. notata and B. canicapilla are allospecies of a single superspecies. Allopatric speciation patterns based on alternate fragmentations and unitings of forests can be drawn from present knowledge of African forest history in relation to Pleistocene-Holocene events. However, a brief review of recent data on interspecific genetic differentiation in birds suggests an important discrepancy between biogeographical and molecular time calibrations. The development of molecular studies appears as a priority for the understanding of the evolution of African tropical forests birds.     

Species tree inference in a recent radiation of orioles (Genus Icterus): multiple markers and methods reveal cytonuclear discordance in the northern oriole group

Recent computational advances provide novel opportunities to infer species trees based on multiple independent loci. Thus, single gene trees no longer need suffice as proxies for species phylogenies. Several methods have been developed to deal with the challenges posed by incomplete and stochastic lineage sorting. In this study, we employed four Bayesian methods to infer the phylogeny of a clade of 11 recently diverged oriole species within the genus Icterus. We obtained well-resolved and mostly congruent phylogenies using a set of seven unlinked nuclear intron loci and sampling multiple individuals per species. Most notably, Bayesian concordance analysis generally agreed well with concatenation; the two methods agreed fully on eight of nine nodes. The coalescent-based method ^∗BEAST further supported six of these eight nodes. The fourth method used, BEST, failed to converge despite exhaustive efforts to optimize the tree search. Overall, the results obtained by new species tree methods and concatenation generally corroborate our findings from previous analyses and data sets. However, we found striking disagreement between mitochondrial and nuclear DNA involving relationships within the northern oriole group. Our results highlight the danger of reliance on mtDNA alone for phylogenetic inference. We demonstrate that in spite of low variability and incomplete lineage sorting, multiple nuclear loci can produce largely congruent phylogenies based on multiple species tree methods, even for very closely-related species.     

On the genetic diversity in the mitochondrial 12S rRNA gene of Platymantis frogs from Western New Guinea (Anura: Ceratobatrachidae)

Platymantis is a group of neobatrachian frogs that occurs from the Philippines to New Guinea – an area situated at the interface between the Australian and Asian biogeographical region that is highly fragmented by stretches of open sea. Partial sequences of the mitochondrial 12S rRNA gene are herein used to infer the relationships of species from the Indonesian part of New Guinea (Papua and West Papua Province). The phylogenetic trees reveal a deep bifurcation between the Asian and Western New Guinean clades being consistent with phylogeographic patterns observed in various other faunal groups. While most species are well differentiated in the examined locus, low interspecific genetic distances between one and three percent were observed in the New Guinean species Platymantis papuensis and P. cryptotis as well as P. pelewensis from Palau. Platymantis papuensis and P. pelewensis are geographically separated from each other by a 1100 km stretch of open sea. The minor degree of genetic differentiation between both species points to a recent event of transmarine dispersal as causation for the occurrence of P. pelewensis on Palau. The low genetic differentiation between P. cryptotis and the sympatric P. papuensis, two species that are bioacoustically and morphologically distinct, may indicate its possibly recent evolutionary origin or, alternatively, yet undetected hybridization between the two species. The same may also hold true for frogs from Yapen that exhibit calls different from the sympatric P. papuensis. Tentatively referred to as Platymantis spec., these frogs are also genetically not well differentiated. It is furthermore concluded that the partly low genetic differentiation of the New Guinean Platymantis species render this group one of the cases in which DNA barcoding would likely fail to produce reliable results.     

Phylogeographic analysis of the green python,Morelia viridis,reveals cryptic diversity

Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test whether significantly differentiated populations occur within the species range. Phylogenetic analysis of mtDNA sequences revealed hierarchal phylogeographic structure both within New Guinea and between New Guinea and Australia. Strongly supported reciprocally monophyletic mitochondrial lineages, northern and southern, were found either side of the central mountain range that runs nearly the length of New Guinea. Limited allozyme data suggest that population differentiation is reflected in the nuclear as well as the mitochondrial genome. A previous morphological analysis did not find any phenotypic concordance with the pattern of differentiation observed in the molecular data. The southern mitochondrial lineage includes all of the Australian haplotypes, which form a single lineage, nested among the southern New Guinean haplotypes.     

The “tropical lineage” of the brown dog tick Rhipicephalus sanguineus sensu lato identified as Rhipicephalus linnaei ()

The brown dog tick (Rhipicephalus sanguineus) parasitises dogs. Over the past decade, two distinct lineages have been recognised – R. sanguineus sensu lato “temperate lineage” and R. sanguineus sensu lato “tropical lineage”. The nominal taxon R. sanguineus (Latreille, 1806) was recently associated with the “temperate lineage”. We here identify the “tropical lineage” as Rhipicephalus linnaei (Audouin, 1826) using material from Australia, where no other Rhipicephalus species parasitises dogs. Whole genome sequencing of R. linnaei from Australia, Fiji and Laos, and assembly of their complete mitochondrial DNA (~15 kb) confirms the genetic identity and distinctness from all other known species within the brown dog tick species complex. Designation of the species R. linnaei is unequivocally supported by material available through the Australian National Insect Collection, Australia. Accordingly, we are formally justified in using R. linnaei for the “tropical lineage”.     

Local versus regional species richness in tropical insects: one lowland site compared with the island of New Guinea

1. The overlap in species composition of Cercopoidea (Aphrophoridae, Cercopidae, and Machaerotidae), Flatidae, and Ricaniidae between two data sets, an almost exhaustive census from 13 Ficus species and a sample from diverse vegetation in the same area, led to the estimate for local species richness of 111 (SE 11.5) species (45 species of Cercopoidea, 36 species of Flatidae, and 30 species of Ricaniidae) at a lowland rainforest site in New Guinea. 2. Samples restricted to 13 species of Ficus contained 66 species, i.e. 59% of the estimated local species richness. This high proportion probably results from the high proportion of polyphagous and tourist (transient) species in the Cercopoidea, Flatidae, and Ricaniidae. 3. The two largest museum collections of New Guinean insects contained 327 species of Cercopoidea from New Guinea, including 23 of the 34 species collected in the field samples. This overlap led to the estimate of 483 (SE 97.2) species of Cercopoidea present in New Guinea. 4. The species found in the field samples were also 2.6 times more likely to be found in the museum collection than other species. This sampling bias can be due to a positive correlation between species local abundance and geographic distribution and/or similar patterns of species abundance at different sites. 5. The estimate of species richness of Cercopoidea in New Guinea increased to 1222 species when corrected for this sampling bias. Thus, only 4% of the New Guinean species were present locally, in the study area. Such high beta diversity is probably a consequence of the exceptional habitat and vegetation diversity in New Guinea, as well as its complex geological history.     

First record of the filefish,Pervagor nigrolineatus,from Japan

A specimen of the filefish,Pervagor nigrolineatus, was collected from dead coral patches at a depth of 3 m in Zamami-jima, Kerama Islands (26° 14′ N, 127° 19′ E). This species is recorded for the first time from Japan. It has been known to be distributed in the tropical western Pacific from the Philippines to New Guinea (Hutchins, 1986). The present specimen is more similar in scale characters to the Philippine specimens than to the New Guinean ones.     

A Phylogeny and Timescale for the Evolution of Pseudocheiridae (Marsupialia: Diprotodontia) in Australia and New Guinea

Pseudocheiridae (Marsupialia: Diprotodontia) is a family of endemic Australasian arboreal folivores, more commonly known as ringtail possums. Seventeen extant species are grouped into six genera (Pseudocheirus, Pseudochirulus, Hemibelideus, Petauroides, Pseudochirops, Petropseudes). Pseudochirops and Pseudochirulus are the only genera with representatives on New Guinea and surrounding western islands. Here, we examine phylogenetic relationships among 13 of the 17 extant pseudocheirid species based on protein-coding portions of the ApoB, BRCA1, ENAM, IRBP, Rag1, and vWF genes. Maximum parsimony, maximum likelihood, and Bayesian methods were used to estimate phylogenetic relationships. Two different relaxed molecular clock methods were used to estimate divergence times. Bayesian and maximum parsimony methods were used to reconstruct ancestral character states for geographic provenance and maximum elevation occupied. We find robust support for the monophyly of Pseudocheirinae (Pseudochirulus + Pseudocheirus), Hemibelidinae (Hemibelideus + Petauroides), and Pseudochiropsinae (Pseudochirops + Petropseudes), respectively, and for an association of Pseudocheirinae and Hemibelidinae to the exclusion of Pseudochiropsinae. Within Pseudochiropsinae, Petropseudes grouped more closely with the New Guinean Pseudochirops spp. than with the Australian Pseudochirops archeri, rendering Pseudochirops paraphyletic. New Guinean species belonging to Pseudochirops are monophyletic, as are New Guinean species belonging to Pseudochirulus. Molecular dates and ancestral reconstructions of geographic provenance combine to suggest that the ancestors of extant New Guinean Pseudochirops spp. and Pseudochirulus spp. dispersed from Australia to New Guinea ∼12.1–6.5 Ma (Pseudochirops) and ∼6.0–2.4 Ma (Pseudochirulus). Ancestral state reconstructions support the hypothesis that occupation of high elevations (>3000 m) is a derived feature that evolved on the terminal branch leading to Pseudochirops cupreus, and either evolved in the ancestor of Pseudochirulus forbesi, Pseudochirulus mayeri, and Pseudochirulus caroli, with subsequent loss in P. caroli, or evolved independently in P. mayeri and P. forbesi. Divergence times within the New Guinean Pseudochirops clade are generally coincident with the uplift of the central cordillera and other highlands. Diversification within New Guinean Pseudochirulus occurred in the Plio-Pleistocene after the establishment of the Central Range and other highlands.     

Cryptic diversity,pathogenicity, and evolutionary species boundaries in Cercospora populations associated with Cercospora leaf spot of Beta vulgaris

The taxonomy and evolutionary species boundaries in a global collection of Cercospora isolates from Beta vulgaris was investigated based on sequences of six loci. Species boundaries were assessed using concatenated multi-locus phylogenies, Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Processes (PTP), and Bayes factor delimitation (BFD) framework. Cercospora beticola was confirmed as the primary cause of Cercospora leaf spot (CLS) on B. vulgaris. Cercospora apii, C. cf. flagellaris, Cercospora sp. G, and C. zebrina were also identified in association with CLS on B. vulgaris. Cercospora apii and C. cf. flagellaris were pathogenic to table beet but Cercospora sp. G and C. zebrina did not cause disease. Genealogical concordance phylogenetic species recognition, GMYC and PTP methods failed to differentiate C. apii and C. beticola as separate species. On the other hand, multi-species coalescent analysis based on BFD supported separation of C. apii and C. beticola into distinct species; and provided evidence of evolutionary independent lineages within C. beticola. Extensive intra- and intergenic recombination, incomplete lineage sorting and dominance of clonal reproduction complicate evolutionary species recognition in the genus Cercospora. The results warrant morphological and phylogenetic studies to disentangle cryptic speciation within C. beticola.     

A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting

Background

Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4–12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species.

Methodology and Principal Findings

(1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test.

Conclusions

We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches–gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus.