Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences

The rodent family Muridae is the single most diverse family of mammals with over 1300 recognized species. We used DNA sequences from the first exon ( approximately 1200bp) of the IRBP gene to infer phylogenetic relationships within and among the major lineages of muroid rodents. We included sequences from every recognized muroid subfamily except Platacanthomyinae and from all genera within the endemic Malagasy subfamily Nesomyinae, all recognized tribes of Sigmodontinae, and a broad sample of genera in Murinae. Phylogenetic analysis of the IRBP data suggest that muroid rodents can be sorted into five major lineages: (1) a basal clade containing the fossorial rodents in the subfamilies Spalacinae, Myospalacinae, and Rhizomyinae, (2) a clade of African and Malagasy genera comprising the subfamilies Petromyscinae, Mystromyinae, Cricetomyinae, Nesomyinae, and core dendromurines, (3) a clade of Old World taxa belonging to Murinae, Otomyinae, Gerbillinae, Acomyinae, and Lophiomyinae, (4) a clade uniting the subfamilies Sigmodontinae, Arvicolinae, and Cricetinae, and (5) a unique lineage containing the monotypic Calomyscinae. Although relationships among the latter four clades cannot be resolved, several well-supported supergeneric groupings within each are identified. A preliminary examination of molar tooth morphology on the resulting phylogeny suggests the triserial murid molar pattern as conceived by evolved at least three times during the course of muroid evolution.     

Ecomorphological diversification following continental colonization in muroid rodents (Rodentia: Muroidea)

The emergence of exceptionally diverse clades is often attributed to ecological opportunity. For example, the exceptional diversity in the most diverse superfamily of mammals, muroid rodents, has been explained in terms of multiple independent adaptive radiations. If multiple ecological opportunity events are responsible for generating muroid diversity, we expect to find evidence of these lineages ecologically diversifying following dispersal into new biogeographical areas. In the present study, we tested the trait‐based predictions of ecological opportunity using data on body size, appendages, and elevation in combination with previously published data on biogeographical transitions and a time‐calibrated molecular phylogeny. We identified weak to no support of early ecological diversification following the initial colonizations of all continental regions, based on multiple tests, including node height tests, disparity through time plots, evolutionary model comparison, and Bayesian analysis of macroevolutionary mixtures. Clades identified with increased diversification rates, not associated with geographical transitions, also did not show patterns of phenotypic divergence predicted by ecological opportunity, which suggests that phylogenetic diversity and phenotypic disparity may be decoupled in muroids. These results indicate that shifts in diversification rates and biogeographically‐mediated ecological opportunity are poor predictors of phenotypic diversity patterns in muroids.     

Evolutionary history of the most speciose mammals: molecular phylogeny of muroid rodents

Phylogenetic relationships between 32 species of rodents representing 14 subfamilies of Muridae and four subfamilies of Dipodidae were studied using sequences of the nuclear protein-coding genes Lecithin Cholesterol Acyl Transferase (LCAT) and von Willebrand Factor (vWF). An examination of some evolutionary properties of each data matrix indicates that the two genes are rather complementary, with lower rates of nonsynonymous substitutions for LCAT. Both markers exhibit a wide range of GC3 percentages (55%-89%), with several taxa above 70% GC3 for vWF, which indicates that those exonic regions might belong to the richest class of isochores. The primary sequence data apparently harbor few saturations, except for transitions on third codon positions for vWF, as indicated by comparisons of observed and expected pairwise values of substitutions. Phylogenetic trees based on 1,962 nucleotidic sites from the two genes indicate that the 14 Muridae subfamilies are organized into five major lineages. An early isolation leads to the clade uniting the fossorial Spalacinae and semifossorial Rhizomyinae with a strong robustness. The second lineage includes a series of African taxa representing nesomyines, dendromurines, cricetomyines, and the sole living member of mystromyines. The third one comprises only the mouselike hamster CALOMYSCUS: The fourth clade represents the cricetines, myospalacines, sigmodontines, and arvicolines, whereas the fifth one comprises four "traditional" subfamilies (Gerbillinae, Murinae, Otomyinae, and Acomyinae). Within these groups, we confirm the monophyly of almost all studied subfamilies, namely, Spalacinae, Rhizomyinae, Nesomyinae, Cricetomyinae, Arvicolinae, Sigmodontinae, Cricetinae, Gerbillinae, Acomyinae, and Murinae. Finally, we present evidence that the sister group of Acomyinae is Gerbillinae, and we confirm a nested position of Myospalacinae within Cricetinae and Otomyinae within Murinae. From a biogeographical point of view, the five main lineages spread and radiated from Asia with different degrees of success: the first three groups are now represented by a limited number of species and genera localized in some regions, whereas the last two groups radiated in a large variety of species and genera dispersed all over the world.     

Molecular phylogeny of European muroid rodents based on complete cytochrome b sequences

Phylogenetic relationships among 18 species of mainly European muroid rodents that belong to three subfamilies were estimated using complete sequences of the mitochondrial cytochrome b gene. The inferred monophyly of the subfamilies Murinae (mice and rats) and Arvicolinae (voles, lemmings, and muskrats) is in agreement with previous studies. Within the Murinae, the morphology-based division of the genus Apodemus into three subgenera is supported by these DNA sequence data. The relationships among the different genera of the Murinae were generally poorly resolved, and the relationships of Micromys and Acomys to the other murine genera remained unresolved. Within the subfamily Arvicolinae, the relations of the genera Arvicola, Clethrionomys, and Microtus remained tentative with our data. However, within the Microtus group, there is a good molecular support for the phylogenetic relationships. These findings suggest that the origin of the different murine and arvicoline lineages was rapid, indicating an adaptive radiation with fast speciation.     

Evolution of the spermatozoon in muroid rodents

In the rodent superfamily Muroidea, a model for the evolution of sperm form has been proposed in which it is suggested that a hook-shaped sperm head and long tail evolved from a more simple, nonhooked head and short tail in several different subfamilies. To test this model the shape of the sperm head, with particular emphasis on its apical region, and length of sperm tail were matched to a recent phylogeny based on the nucleotide sequence of several protein-coding nuclear genes from 3 families and 10 subfamilies of muroid rodents. Data from the two other myomorph superfamilies, the Dipodoidea and kangaroo rats in the Geomyoidea, were used for an outgroup comparison. In most species in all 10 muroid subfamilies, apart from in the Murinae, the sperm head has a long rostral hook largely composed of acrosomal material, although its length and cross-sectional shape vary across the various subfamilies. Nevertheless, in a few species of various lineages a very different sperm morphology occurs in which an apical hook is lacking. In the outgroups the three species of dipodid rodents have a sperm head that lacks a hook, whereas in the heteromyids an acrosome-containing apical hook is present. It is concluded that, as the hook-shaped sperm head and long sperm tail occur across the muroid subfamilies, as well as in the heteromyid rodents, it is likely to be the ancestral condition within each of the subfamilies with the various forms of nonhooked sperm heads, that are sometimes associated with short tails, being highly derived states. These findings thus argue against a repeated evolution in various muroid lineages of a complex, hook-shaped sperm head and long sperm tail from a more simple, nonhooked sperm head and short tail. An alternative proposal for the evolution of sperm form within the Muroidea is presented in the light of these data.     

Molecular evolutionary relationships of three genera of nesomyinae,endemic rodent taxa from madagascar

The relationships of Nesomyinae, a group of murid rodents endemic to the island of Madagascar, were investigated with two comparative molecular approaches. Compared to those of other muroid rodents representing Murinae, Cricetinae, Cricetomyinae. Arvicolinae, and Sigmodontinae, complete sequences of the 12S rRNA mitochondrial gene suggest that the Malagasy nesomyinesMacrotarsomys andNesomys are monophyletic and that their sister-group among the taxa analyzed isCricetomys. A limited series of DNA/DNA hybridization experiments extends these observations to a third nesomyine genus,Eliurus, and a second cricetomyine taxon,Saccostomus. By relating the amounts of overall genomic divergence with geological time as calibrated by theMus/Rattus dichotomy estimated at 12–14 My, the oldest within-Nesomyinae dichotomy is estimated to be 10.8 to 12.6 My. Thus, these three genera of Malagasy nesomyine rodents appear to be a rather ancient offshoot from African ancestors whose Recent relatives are Cricetomyinae. This preliminary observation should be confirmed by sampling additional genera of nesomyines and additional representatives for other subfamilies of African muroids.     

Multigene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes

Despite its great diversity and biomedical importance, the rodent subfamily Murinae is poorly resolved phylogenetically. We present the first cladistic analysis sampling multiple representatives of most major groups based on DNA sequence for three nuclear (GHR, RAG1, and AP5) and one mitochondrial (COII and parts of COI and ATPase 8) fragments. Analyzed separately, the four partitions agree broadly with each other and the combined analysis. The basal split is between a clade of Philippine Old Endemics and all remaining murines. Within the latter, rapid radiation led to at least seven geographically distinct lineages, including a Southeast Asian Rattus clade; a diverse Australo-Papuan and Philippine clade; an African arvicanthine group including the otomyines; an African Praomys group; and three independent genera from Africa and Asia, Mus, Apodemus, and Malacomys. The murines appear to have originated in Southeast Asia and then rapidly expanded across all of the Old World. Both nuclear exons provide robust support at all levels. In contrast, the bootstrap proportions from mitochondrial data decline rapidly with increasing depth in the tree, together suggesting that nuclear genes may be more useful even for relatively recent divergences (< 10MYA).     

The evolutionary history of Eryngium (Apiaceae, Saniculoideae): rapid radiations, long distance dispersals, and hybridizations

Eryngium is the largest and arguably the most taxonomically complex genus in the family Apiaceae. Infrageneric relationships within Eryngium were inferred using sequence data from the chloroplast DNA trnQ-trnK 5'-exon and nuclear ribosomal DNA ITS regions to test previous hypotheses of subgeneric relationships, explain distribution patterns, reconstruct ancestral morphological features, and elucidate the evolutionary processes that gave rise to this speciose genus. In total, 157 accessions representing 118 species of Eryngium, 15 species of Sanicula (including the genus Hacquetia that was recently reduced to synonymy) and the monotypic Petagnaea were analyzed using maximum parsimony and Bayesian methods. Both separate and simultaneous analyses of plastid and nuclear data sets were carried out because of the prevalence of polyploids and hybrids within the genus. Eryngium is confirmed as monophyletic and is divided into two redefined subgenera: Eryngium subgenus Eryngium and E. subgenus Monocotyloidea. The first subgenus includes all examined species from the Old World (Africa, Europe, and Asia), except Eryngium tenue, E. viviparum, E. galioides, and E. corniculatum. Eryngium subgenus Monocotyloidea includes all examined species from the New World (North, Central and South America, and Australia; herein called the "New World sensu stricto" clade) plus the aforementioned Old World species that fall at the base of this clade. Most sectional and subgeneric divisions previously erected on the basis of morphology are not monophyletic. Within the "New World sensu stricto" group, six clades are well supported in analyses of plastid and combined plastid and nuclear data sets; the relationships among these clades, however, are unresolved. These clades are designated as "Mexican", "Eastern USA", "South American", "North American monocotyledonous", "South American monocotyledonous", and "Pacific". Members of each clade share similar geographical distributions and/or morphological or ecological traits. Evidence from branch lengths and low sequence divergence estimates suggests a rapid radiation at the base of each of these lineages. Conflict between chloroplast and nuclear data sets is weak, but the disagreements found are suggestive that hybrid speciation in Eryngium might have been a cause, but also a consequence, of the different rapid radiations observed. Dispersal-vicariance analysis indicates that Eryngium and its two subgenera originated from western Mediterranean ancestors and that the present-day distribution of the genus is explained by several dispersal events, including one trans-Atlantic dispersal. In general, these dispersals coincide with the polytomies observed, suggesting that they played key roles in the diversification of the genus. The evolution of Eryngium combines a history of long distance dispersals, rapid radiations, and hybridization, culminating in the taxonomic complexity observed today in the genus.     

An endemic radiation of Malagasy songbirds is revealed by mitochondrial DNA sequence data

The bird fauna of Madagascar includes a high proportion of endemic species, particularly among passerine birds (Aves: Passeriformes). The endemic genera of Malagasy songbirds are not allied obviously with any African or Asiatic taxa, and their affinities have been debated since the birds first were described. We used mitochondrial sequence data to estimate the relationships of 13 species of endemic Malagasy songbirds, 17 additional songbird species, and one species of suboscine passerine. In our optimal trees, nine of the 13 Malagasy species form a clade. although these birds currently are classified in three different families. In all optimal trees, the sister to this endemic clade is a group of Old World warblers including both African and Malagasy birds. The endemic Malagasy songbird clade rivals other island radiations, including the vangas of Madagascar and the finches of the Galapagos, in ecological diversity.     

Molecular Phylogeny of Rodents, with Special Emphasis on Murids: Evidence from Nuclear Gene LCAT

Phylogenetic relationships among 19 extant species of rodents, with special emphasis on rats, mice, and allied Muroidea, were studied using sequences of the nuclear protein-coding gene LCAT (lecithin:cholesterol acyltransferase), an enzyme of cholesterol metabolism. Analysis of 705 base pairs from the exonic regions of LCAT confirmed known groupings in and around Muroidea. Strong support was found for the families Sciuridae (squirrel and marmot) and Gliridae (dormice) and for suprafamilial taxa Muroidea and Caviomorpha (guinea pig and allies). Within Muroidea, the first branching leads to the fossorial mole rats Spalacinae and bamboo rats Rhizomyinae. The other Muroidea appear as a polytomy from which are issued Gerbillinae (gerbils), Murinae (rats and mice), Sigmodontinae (New World cricetids), Cricetinae (hamsters), and Arvicolinae (voles). Evidence from LCAT sequences agrees with that from a number of previous molecular and morphological studies, both concerning branching orders inside Muroidea and the bush-like radiation of rodent suprafamilial taxa (caviomorphs, sciurids, glirids, muroids), thus suggesting that this nuclear gene is an appropriate candidate for addressing questions of rodents relationships.     

Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes

Background

Within the subfamily Murinae, African murines represent 25% of species biodiversity, making this group ideal for detailed studies of the patterns and timing of diversification of the African endemic fauna and its relationships with Asia. Here we report the results of phylogenetic analyses of the endemic African murines through a broad sampling of murine diversity from all their distribution area, based on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR).

Results

A combined analysis of one mitochondrial and two nuclear gene sequences consistently identified and robustly supported ten primary lineages within Murinae. We propose to formalize a new tribal arrangement within the Murinae that reflects this phylogeny. The diverse African murine assemblage includes members of five of the ten tribes and clearly derives from multiple faunal exchanges between Africa and Eurasia. Molecular dating analyses using a relaxed Bayesian molecular clock put the first colonization of Africa around 11 Mya, which is consistent with the fossil record. The main period of African murine diversification occurred later following disruption of the migration route between Africa and Asia about 7–9 Mya. A second period of interchange, dating to around 5–6.5 Mya, saw the arrival in Africa of Mus (leading to the speciose endemic Nannomys), and explains the appearance of several distinctive African lineages in the late Miocene and Pliocene fossil record of Eurasia.

Conclusion

Our molecular survey of Murinae, which includes the most complete sampling so far of African taxa, indicates that there were at least four separate radiations within the African region, as well as several phases of dispersal between Asia and Africa during the last 12 My. We also reconstruct the phylogenetic structure of the Murinae, and propose a new classification at tribal level for this traditionally problematic group.     

Mitochondrial DNA Evidence and Evolution in Varanoidea (Squamata)

Varanoidea is a monophyletic group of anguimorph lizards, comprising the New World helodermatids, the Bornean earless monitor Lanthanotus borneensis , and the Old World monitors ( Varanus ). I use mitochondrial DNA sequences and extensive taxonomic sampling to test alternative hypotheses of varanoid relationships. The most parsimonious hypothesis confirms the monophyly of Varanoidea ( Heloderma, Lanthanotus , and Varanus ) and Varanus , as well as the sister-taxon relationship of Varanus and Lanthanotus . The relationships among Varanus species differ in several respects from previous hypotheses. Three major lineages are recognized within Varanus : an African clade basal to the rest of the group, an Indo-Asian clade, and an Indo-Australian clade. Within the last lineage, the endemic Australian dwarf monitors ( Odatria ) form a clade sister to the large Australian monitors (the gouldii group). Tests of the effects of rate heterogeneity and homoplasy demonstrate that putative process partitions of data are largely congruent with one another and contribute positive support to the overall hypothesis.     

Timing and tempo of early and successive adaptive radiations in Macaronesia

The flora of Macaronesia, which encompasses five Atlantic archipelagos (Azores, Canaries, Madeira, Cape Verde, and Salvage), is exceptionally rich and diverse. Spectacular radiation of numerous endemic plant groups has made the Macaronesian islands an outstanding area for studies of evolution and speciation. Despite intensive investigation in the last 15 years, absolute age and rate of diversification are poorly known for the flora of Macaronesia. Here we report molecular divergence estimates and rates of diversification for five representative, putative rapid radiations of monophyletic endemic plant lineages across the core eudicot clade of flowering plants. Three discrete windows of colonization during the Miocene and early Pliocene are suggested for these lineages, all of which are inferred to have had a single colonization event followed by rapid radiation. Subsequent inter-archipelago dispersal events into Madeira and the Cape Verdes took place very recently during the late Pliocene and Pleistocene after initial diversification on the Canary Islands. The tempo of adaptive radiations differs among the groups, but is relatively rapid compared to continental and other island radiations. Our results demonstrate that opportunity for island colonization and successful radiation may have been constrained to discrete time periods of profound climatic and geological changes in northern African and the Mediterranean.     

Molecular phylogeny and morphological homoplasy in fruitbats.

The present study evaluates the evolutionary framework of the Old World fruitbats based on the cytochrome b and 16S rRNA mitochondrial gene sequences from a wide range of taxa. Phylogenetic analyses indicated that morphology-based subfamilies and most suprageneric groups are nonnatural assemblages. They also support the existence of an endemic African clade of fruitbats. The discrepancy between the evolutionary relationships yielded by molecular and morphological data sets may be, at least in part, explained by the recurrent retention of primitive morphology (Rousettus-like) across different lineages. The maintenance of primitive characters in different groups of flying foxes, as well as morphological convergence in nectar-feeding bats and possibly also in short-muzzle bats, may have led to high levels of homoplasy, resulting in misleading taxonomic arrangements. This may be particularly so with respect to high taxonomic levels based on morphological characters.     

The bushlike radiation of muroid rodents is exemplified by the molecular phylogeny of the LCAT nuclear gene

Phylogenetic relationships among 40 extant species of rodents, with an emphasis on the taxonomic sampling of Muridae and Dipodidae, were studied using sequences of the nuclear protein-coding gene LCAT (lecithin cholesterol acyl transferase). Analysis of 804 bp from the exonic regions of LCAT confirmed many traditional groupings in and around Muridae. A strong support was found for the families Muridae (represented by 29 species) and Dipodidae (5 species). Compared with Sciuridae, Gliridae, and Caviomorpha, the Dipodidae family appeared the closest relative of Muridae, confirming the suprafamilial Myodonta concept. Within the speciose family Muridae, the first branching leads to the fossorial Spalacinae and semifossorial Rhyzomyinae. The remaining components of Muridae appear as a polytomy from which are issued Sigmodontinae, Calomyscinae, Arvicolinae, Cricetinae, Mystromyinae, Nesomyinae, and some Dendromurinae (Steatomys and Dendromus). This phylogeny is interpreted as the result of a bushlike radiation at the end of the early Miocene, leading to emergence of most living subfamilies. The separation between three additional taxa, Murinae, Gerbillinae, and "Acomyinae" (which comprises the genera Acomys, Deomys, Uranomys, and Lophuromys), has occurred more recently from a common ancestor issued from the main basal radiation. As previously shown by other molecular studies, the vlei rats, Otomyinae, are nested within Old World Murinae. In the same way, the zokors, Myospalacinae, appear strongly nested within the hamsters, Cricetinae. Finally, we propose a sister group relationship between Malagasy Nesomyinae and south African Mystromyinae.     

Molecular insights into the evolution of the family Bovidae: a nuclear DNA perspective.

The evolutionary history of the family Bovidae remains controversial despite past comprehensive morphological and genetic investigations. In an effort to resolve some of the systematic uncertainties within the group, a combined molecular phylogeny was constructed based on four independent nuclear DNA markers (2,573 characters) and three mitochondrial DNA genes (1,690 characters) for 34 bovid taxa representing all seven of the currently recognized bovid subfamilies. The nuclear DNA fragments were analyzed separately and in combination after partition homogeneity tests were performed. There was no significant rate heterogeneity among lineages, and retention index values indicated the general absence of homoplasy in the nuclear DNA data. The conservative nuclear DNA data were remarkably effective in resolving associations among bovid subfamilies, which had a rapid radiation dating back to approximately 23 MYA. All analyses supported the monophyly of the Bovinae (cow, nilgai, and kudu clade) as a sister lineage to the remaining bovid subfamilies, and the data convincingly suggest that the subfamilies Alcelaphinae (hartebeest, tsessebe, and wildebeest group) and Hippotraginae (roan, sable, and gemsbok clade) share a close evolutionary relationship and together form a sister clade to the more primitive Caprinae (represented by sheep, goat, and muskox). The problematic Reduncinae (waterbuck, reedbuck) seem to be the earliest-diverging group of the Caprinae/Alcelaphinae/Hippotraginae clade, whereas the Antilopinae (gazelle and dwarf antelope clade) were always polyphyletic. The sequence data suggest that the initial diversification of the Bovidae took place in Eurasia and that lineages such as the Cephalophinae and other enigmatic taxa (impala, suni, and klipspringer) most likely originated, more or less contemporaneously, in Africa.     

Piecing together the "new" Plantaginaceae

Scrophulariaceae is one of the families that has been divided extensively due to the results of DNA sequence studies. One of its segregates is a vastly enlarged Plantaginaceae. In a phylogenetic study of 47 members of Plantaginaceae and seven outgroups based on 3561 aligned characters from four DNA regions (the nuclear ribosomal ITS region and the plastid trnL-F, rps16 intron, and matK-trnK intron regions), the relationships within this clade were analyzed. The results from parsimony and Bayesian analyses support the removal of the Lindernieae from Gratioleae to a position outside Plantaginaceae. A group of mainly New World genera is paraphyletic with respect to a clade of Old World genera. Among the New World taxa, those offering oil as a pollinator reward cluster together. Ourisia is sister to this clade. Gratioleae consist of Gratiola, Otacanthus, Bacopa, Stemodia, Scoparia, and Mecardonia. Cheloneae plus Russelia and Tetranema together constitute the sister group to a clade predominantly composed of Old World taxa. Among the Old World clade, Ellisiophyllum and Lafuentea have been analyzed for the first time in a molecular phylogenetic analysis. The former genus is sister to Sibthorpia and the latter is surprisingly the sister to Antirrhineae.     

Phylogenetic relationships of wild silkmoths (Lepidoptera: Saturniidae) inferred from four protein-coding nuclear genes

Abstract.  The Saturniidae, or wild silkmoths, number approximately 1861 species in 162 genera and nine subfamilies including Cercophaninae and Oxyteninae. They include some of the largest and most spectacular of all Lepidoptera, such as the moon or luna moths, atlas moths, emperor moths, and many others. Saturniids have been important as sources of wild silk and/or human food in a number of cultures, and as models for comparative studies of genetics, development, physiology, and ecology. Seeking to improve the phylogenetic framework for such studies, we estimated relationships across Saturniidae, sampling all nine subfamilies plus all five tribes of Saturniinae. Seventy-five exemplars (45 Saturniidae plus 30 bombycoid outgroups) were sequenced for four protein-coding nuclear gene regions (5625 bp total), namely CAD (the fusion protein carbamoylphosphate synthetase/aspartate transcarbamylase/dihydroorotase), DDC (dopa decarboxylase), period, and wingless. The data, analyzed by parsimony and likelihood, gave a strongly resolved phylogeny at all levels. Relationships among subfamilies largely mirrored the pre-cladistic hypothesis of Michener, albeit with significant exceptions, and there was definitive support for the morphology-based proposal that Ludiinae form a tribe (Micragonini) within Saturniinae. In the latter subfamily, the African tribe Urotini was shown to be paraphyletic with respect to Bunaeini and Micragonini, also in accord with recent morphological findings. Relationships within the New World subfamilies Arsenurinae, Ceratocampinae and Hemileucinae nearly always accord with previous morphology-based phylogenies when both are clearly resolved. Within Hemileucinae, Hemileucini are paraphyletic with respect to the monotypic Polythysanini. A preliminary biogeographical analysis supports ancestral restriction to the New World, followed by dispersal and/or vicariance splitting most of the family into a largely New World versus a largely Old World clade.     

The phylogenetic position of "Acomyinae" (Rodentia, Mammalia) as sister group of a Murinae + Gerbillinae clade: evidence from the nuclear ribonuclease gene.

The phylogenetic relationships of Acomys and Uranomys within Muridae were investigated using nuclear pancreatic ribonuclease A gene sequences. The various kinds of substitutions in the data matrix (15 taxa x 375 nucleotides) were examined for saturation, in order to apply a weighted parsimony approach. Phylogenies were derived by maximum parsimony (weighted and unweighted) and maximum likelihood procedures, using a dormouse (Gliridae) as outgroup. Maximum likelihood gave the most robust results. All analyses cluster some traditional taxa with a strong robustness, such as three species of the genus Mus, two South-East Asian rats, and two genera in each of the gerbil and vole families. When analyzed with those of other murid rodents representing Murinae, Gerbillinae, Arvicolinae, Cricetinae, and Sigmodontinae, sequences of the ribonuclease gene suggest that Acomys and Uranomys constitute a monophyletic clade at the subfamily level, denoted "Acomyinae." The relationships between the six subfamilies of Muridae appear poorly resolved, except for a clade uniting Murinae, Acomyinae, and Gerbillinae. Within this clade, the sister group of Acomyinae could not be identified, as the branch length defining a Gerbillinae + Murinae cluster is extremely short. The poor resolution of our phylogenetic inferences is probably the result of two confounding factors, namely the limited size of the pancreatic ribonuclease sequence and the probable short time intervals during the radiation of the six murid subfamilies involved in this study.     

Pliocene colonization and adaptive radiations in Australia and New Guinea (Sahul): multilocus systematics of the old endemic rodents (Muroidea: Murinae)

The old endemic rodents of Australia and New Guinea (Sahul) represent one or more large adaptive radiations including novel morphological adaptations to aquatic, arboreal, hopping, and arid ecologies. Four tribes recognized among the Sahulian old endemics (Hydromini, Conilurini, Anisomyini, and Uromyini) reflect distinct biogeographic and ecomorphological hypotheses about diversification within the Old Endemics. We present the first character-based phylogeny of the Sahulian Old Endemic rodents with broad sampling, nested within a broader phylogeny of the Murinae. We estimated phylogenies from >2,500 nucleotides of mtDNA sequence and >9,500 nucleotides from six autosomal nuclear loci, for individual genes and for the full concatenated data using parsimony, likelihood, and Bayesian methods. Our results strongly supported monophyly of the group and its sister relationship to the Philippine old endemics of the Chrotomys division. Most striking was the rapid diversification after the Late Miocene or Early Pliocene colonization of New Guinea from the west, consistent with a single colonization of the Sahulian continent. That was followed 2-3 My later by a second adaptive radiation resulting from one or more colonizations of Australia. Monophyly was not supported for the Anisomyini or the Conilurini but was for the Uromyini nested within the Conilurini and for the Hydromyini. Conflict among gene phylogenies was weak, and support for the consensus topology increased with more (even conflicting) data.