Molecular phylogeny of Mugilidae fishes revised

Systematics derived from morphological characters often does not correspond with the evolutionary processes underlying the divergence within a group of organisms. In the family Mugilidae (Teleostei) morphological similarities have resulted in inconsistencies between taxonomy and phylogeny among its species, and particularly for the genera Mugil, Liza and Chelon where both intrageneric and intergeneric phylogenetic clarifications are needed. To address these issues, the direct sequencing of the mitochondrial region that encodes Phenylalanine (69 bp), 12S rRNA (842 bp), cytochrome c oxidase subunit I (651 bp) and cytochrome b (702 bp) was carried out. The data reveal that Mugil platanus and Mugil liza represent a continuum of a single species, closely related to but distinct from Mugil cephalus which itself appears to comprise a grouping of multiple and closely related species. This species complex was genetically distinct from Mugil curema, which, based on three clearly diverged species identified in this study along the Atlantic coast of the Americas, requires extensive taxonomic revision throughout its world-wide distribution. Unlike the monophyly supported within Mugil, relationships within Liza are paraphyletic, and a taxonomic revision of the genera Liza, Chelon and Oedalechilus is needed.     

Evolution and phylogeny of old world deer

The phylogenetic pattern and timing of the radiation of Old World deer was determined based on the complete mitochondrial cytochrome b gene from 33 Cervinae taxa. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with muntjacs as sister group as well as for the divergence of at least three distinct genera: Rucervus, Dama, and Cervus. The latter clade comprises what have previously been regarded as the genera or subgenera Panolia, Rusa, Cervus, Sika, and probably Przewalskium. Our data also consistently confirmed paraphyly of nominate C. elaphus and did not support the monophyly of Axis. We used these molecular phylogenies to assess the homoplastic evolution of morphological, geographical, ecological, and selected behavioural character state differences within the Cervinae. Reliable fossil calibrations, large molecular data sets, and improved dating methods are shaping a molecular time scale for the evolutionary radiation of Old World deer that occurred at the Miocene/Pliocene transition and is largely compatible with existing palaeontological evidence. Using node ages estimated from sequence data, we estimated an average per-lineage diversification rate of 0.51+/-0.1 species per million years (my) over roughly the last 6 mya.     

A molecular phylogeny of the Sylvia cantillans complex: cryptic species within the Mediterranean basin

The subalpine warbler Sylvia cantillans is formally considered a polytypic species, with four subspecies, European S. c. cantillans, albistriata, moltonii (recently resumed name: subalpina) and North African S. c. inornata. They are very similar in external morphology but clearly differ in their vocalizations. We evaluated their uncertain taxonomic status reconstructing the phylogenetic and phylogeographic relationships among populations sampled across major biogeographical areas in the European species’ range, using nucleotide sequences of the mitochondrial cytochrome b gene (mtDNA cyt b). A variety of phylogenetic analyses concordantly led to identify four major groups, only partially corresponding to the three European nominal subspecies. Phylogenetic trees showed a monophyletic group including all moltonii individuals, well diverged from all other taxa. Populations taxonomically assigned to cantillans were polyphyletic being split into two distinct clades (western and southern cantillans), with monophyletic albistriata closely related to southern cantillans. Individuals of moltonii and southern cantillans sampled in sites of sympatry in central Italy were assigned to their respective groups, with perfect concordance between phenotypic and genetic identifications. All findings indicate that moltonii should be ranked as a distinct species. Former subspecies cantillans is polyphyletic, but additional data are needed to define the taxonomic status of its two clades. Albistriata is phylogenetically related to southern cantillans and should be provisionally kept as a subspecies of S. cantillans. The cantillans complex thus provides an interesting case-study illustrating geographical structuring across small geographical ranges, and it exemplifies speciation through differentiation in allopatry leading to reproductive isolation after a secondary contact.     

Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences

To explore phylogenetic relationships among glyptosternoid fishes, we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1138 base pair). Thirteen species of glyptosternoid fishes and six species of non-glyptosternoids represent 10 sisorid genera were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, minimum evolution, maximum likelihood, and Bayesian methods. Bayesian and maximum likelihood analyses support the monophyly of glyptosternoids, but our hypothesis of internal relationships differs from previous hypothesis. Results indicated that glyptosternoid is a monophyletic group and genera Glyptosternum and Exostoma are two basal species having a primitive position among it. Genera Euchiloglanis and Pareuchiloglanis form a sister-group. Then they form a sister-group with Pseudexostoma plus Oreoglanis. Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.     

Use of phylogeny to resolve the taxonomy of the widespread and highly polymorphic African giant shrews (Crocidura olivieri group, Crocidurinae, Mammalia)

The aim of this study is to provide a better understanding of the genetic relationships within the widespread and highly polymorphic group of African giant shrews (Crocidura olivieri group). We sequenced 769 base pairs (bp) of the mitochondrial cytochrome b gene and 472 bp of the mitochondrial control region over the entire geographic range from South Africa to Morocco. The analyses reveal four main clades associated with different biomes. The largest clade occurs over a range covering Northwest and Central Africa and includes samples of C. fulvastra, C. olivieri, and C. viaria. The second clade is composed of C. goliath from Gabon, while South African C. flavescens, and C. hirta form two additional clades. On the basis of these results, the validity of some taxa in the C. olivieri group should be re-evaluated.     

Multiple in-to-Africa dispersals of labeonin fishes (Teleostei: Cyprinidae) revealed by molecular phylogenetic analysis

An out-of-Africa dispersal route has been proposed for many organisms, including modern man. However, counter examples of in-to-Africa dispersal routes are less common. In the present article, the phylogenetic relationships within the Labeoninae, a subfamily of cyprinid fishes distributed in Asia and Africa, were analyzed to investigate the biogeographic processes governing the modern distribution of these Asian and African cyprinids. The mitochondrial DNA cytochrome b gene was used as a molecular marker. The phylogenetic analysis indicated that the subfamily Labeoninae is a monophyletic group, with some Asian labeonins located at the basal position. Two subclades were found that contained both African and Asian species, which highlighted a need for further biogeographic analysis. Based on this analysis, it is proposed that the centre of origin of the Labeoninae was in East Asia. Molecular clock estimation suggests that the Labeoninae arose by the Early Miocene (~23 MYA) during the period of the second Tibetan uplift. Subsequently, two dispersal events of labeonins from Asia into Africa occured in the Early Miocene (~ 20 MYA) and Late Miocene (~9 MYA) and serve as examples counter to out-of-Africa dispersal.     

MtDNA phylogeny provides evidence of generic polyphyleticism for East Asian bagrid catfishes

We explore the intrafamilial relationships of East Asian bagrid catfishes (Hemibagrus, Pseudobagrus, Pelteobagrus, and Leiocassis) based on 245 sequences of 1092 bp mitochondrial cytochrome b fragments. Four haplotypes were found to be shared by Pseudobagrus ussuriensis, Pelteobagrus vachelli and Pelteobagrus nitidus. Phylogenetic trees were performed using the neighbor joining, maximum parsimony, maximum likelihood, and Bayesian likelihood methods. The phylogenetic trees based on NJ, MP, ML and BL inferences strongly support polyphyleticism for the currently recognized genera Pseudobagrus, Pelteobagrus and Leiocassis. However, the species currently assigned to these three genera form a robustly monophyletic group with relatively low genetic divergence. The structure of maxillary barbels and serrations on the anterior edge of the pectoral spines seem to be indicatory of appropriate phylogenetic traits. We propose that only Hemibagrus and Pseudobagrus are the only valid genera of East Asian bagrids. Handling editor: K. Martens     

The interpretation of process from pattern using two-dimensional spectral analysis: modelling single species patterns in vegetation

Two-dimensional spectral analyses of spatial patterns are made using (i) the autocorrelation function, (ii) the periodogram, and its polar summary (iii) the R-spectrum and (iv) the -spectrum. Together these give a sensitive analysis of both the complete range of scales of pattern and directional components which exist in data sets and we illustrate how the significance of observed spectral features can be assessed.We investigate the spatial pattern of Calluna vulgaris in a regenerating woodland and of Epilobium angustifolium spreading in a woodland following the thinning of trees. Evidence in the spectra is found for directional, clumping and inhibition patterns, and is discussed in relation to spectra obtained from simulations of known pattern generating processes. Hypotheses about the important biological, environmental and management influences on the structure of the communities are examined.We gratefully acknowledge the Swedish Coniferous Biome Project and Dr P. J. Diggle for access to the heather data.     

Molecular phylogeny and biogeography of woolly flying squirrel (Rodentia: Sciuridae), inferred from mitochondrial cytochrome b gene sequences

To investigate the genetic diversity between the populations of woolly flying squirrels (Eupetaurus) from the eastern and western extremes of the Himalayas, partial mitochondrial cytochrome b gene sequences (390-810 bp) that were determined from the museum specimens were analyzed using maximum parsimony (MP) and maximum likelihood (ML) methods. The molecular data reveal that the two specimens that were collected in northwestern Yunnan (China) are members of the genus Eupetaurus. Reconstructed phylogenetic relationships show that the populations of Eupetaurus in the eastern and western extremes of the Himalayas are two distinct species with significant genetic differences (12%) and diverged about 10.8 million years ago. Eupetaurus is significantly different from Petaurista and Pteromys. The level of estimated pairwise-sequence divergence observed between Eupetaurus and Petaurista or Pteromys is greater than that observed between Eupetaurus and Trogopterus, Belomys, Glaucomys, or Hylopetes. Considering the divergence time of the two Eupetaurus groups, the glaciations and the uplift of the Himalayas and Qinghai-Tibet plateau during the Pliocene-Pleistocene period might be the major factors affecting the present distribution of Eupetaurus along the Himalayas.     

Molecular identification of crocodile species using novel primers for forensic analysis

All crocodilians are under varying degrees of threat due to over exploitation and these species have been listed in Appendix I or II of CITES. The lack of molecular techniques for the identification of confiscated samples makes it difficult to enforce the law. Conclusive forensic identification of species requires a complete gene sequence which is difficult in case of degraded samples. We have developed two novel sets of primers to amplify two partial cytochrome b gene sequences of six crocodile species i.e. Crocodylus palustris, Crocodylus porosus, Crocodylus siamensis, Crocodylus niloticus, Gavialis gangeticus and Caiman crocodilus. These partial sequences were edited to give a complete cyt b gene sequence, which can be used as an effective tool for forensic authentication of crocodile species. A phylogeny of crocodile species was reconstructed using these sequences. The described primers hold great promise in forensic identification of crocodile species, which can aid in the effective enforcement of law and conservation of these ancient species.     

Relationship between mechanomyogram and force during voluntary contractions reinvestigated using spectral decomposition

A mechanomyogram (MMG) is considered to represent the pressure waves resulting from the lateral expansion of contracting muscle fibers. However, the actual MMG recording appears not only to reflect lateral changes of active fibers, but also to include the effect of their longitudinal shortening, because the fiber orientation, particularly in pennate muscles, is not parallel with the MMG transducer attached at the skin surface. In the present investigation, a spectral decomposition method was developed to eliminate the interference due to fiber longitudinal movement from the MMG recording. The MMG was recorded over the belly of the rectus femoris muscle, which is a pennate muscle. Vibration over the tibial tuberosity (VTT) was used as a measure of the integrated longitudinal movement of the muscle fibers. The lateral and longitudinal components included in the MMG were separated by a spectral decomposition method that is based on the coherence function of the MMG and VTT. The MMG/force relationship was compared between the original and decomposed MMG. One-third of the 12 subjects demonstrated a curvilinear relationship between the original MMG and force throughout the range of force. In the other two-thirds, the MMG saturated or reduced beyond 70% of the maximum voluntary contraction (MVC). After decomposition, the MMG increased progressively with force up to 70% MVC, beyond which it decreased in all subjects. The spectral decomposition method described here is considered to be a useful tool with which to examine in more detail the MMG/force relationship of different pennate muscles.     

Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences

Voles of the genus Microtus represent one of the most speciose mammalian genera in the Holarctic. We established a molecular phylogeny for Microtus to resolve contentious issues of systematic relationships and evolutionary history in this genus. A total of 81 specimens representing ten Microtus species endemic to Europe as well as eight Eurasian, six Asian and one Holarctic species were sequenced for the entire cytochrome b gene (1140 bp). A further 25 sequences were retrieved from GenBank, providing data on an additional 23, mainly Nearctic, Microtus species. Phylogenetic analysis of these 48 species generated four well-supported monophyletic lineages. The genus Chionomys, snow voles, formed a distinct and well-supported lineage separate from the genus Microtus. The subgenus Microtus formed the strongest supported lineage with two sublineages displaying a close relationship between the arvalis species group (common voles) and the socialis species group (social voles). Monophyly of the Palearctic pitymyid voles, subgenus Terricola, was supported, and this subgenus was also subdivided into two monophyletic species groups. Together, these groupings clarify long-standing taxonomic uncertainties in Microtus. In addition, the "Asian" and the Nearctic lineages reported previously were identified although the latter group was not supported. However, relationships among the main Microtus branches were not resolved, suggesting a rapid and potentially simultaneous radiation of a widespread ancestor early in the history of the genus. This and subsequent radiations discernible in the cytochrome b phylogeny, show the considerable potential of Microtus for analysis of historical and ecological determinants of speciation in small mammals. It is evident that speciation is an ongoing process in the genus and that the molecular data provides a vital insight into current species limits as well as cladogenic events of the past.     

Horned lizard (Phrynosoma) phylogeny inferred from mitochondrial genes and morphological characters: understanding conflicts using multiple approaches

The genus Phrynosoma includes 13 species of North American lizards characterized by unique and highly derived morphologies and ecologies. Understanding interspecific relationships within this genus is essential for testing hypotheses about character evolution in this group. We analyzed mitochondrial ND4 and cytochrome b gene sequence data from all species of Phrynosoma in conjunction with a previously published dataset including 12S and 16S rRNA gene sequences and morphological characters. We used multiple phylogenetic methods and diagnostic tests for data combinability and taxonomic congruence to investigate the data in separate and combined analyses. Separate data partitions resulted in several well-supported lineages, but taxonomic congruence was lacking between topologies from separate and combined analyses. Partitioned Bremer support analyses also reveals conflict between data partitions in certain tree regions. When taxa associated with well-supported clades were removed from analyses, phylogenetic signal was lost. Combined, our results initially suggest conflict between data partitions, but further tests show the data are only appropriate for phylogenetic reconstruction of those parts of the topology that were well resolved. Nonetheless, our data analyses reveal five well-supported clades: (1) Phrynosoma ditmarsi and Phrynosoma hernandesi, (2) P. ditmarsi, P. hernandesi, and Phrynosoma douglasii, (3) P. ditmarsi, P. hernandesi, P. douglasii, and Phrynosoma orbiculare, (4) Phrynosoma mcallii and Phrynosoma platyrhinos, and (5) Phrynosoma braconnieri and Phrynosoma taurus.     

Molecular phylogeny of two lineages of Leuciscinae cyprinids (Telestes and Scardinius) from the peri-Mediterranean area based on cytochrome b data

We examined phylogenetic relationships in two lineages of Leuciscinae cyprinid fishes based on the sequence data of the complete mitochondrial DNA region coding for the cytochrome b gene (1140 bp). Telestes includes obligate riverine, moderately cold water-adapted species whereas Scardinius comprises warm-adapted species living in lowland lakes and still waters of rivers and streams. We also analysed selected representatives of Leuciscus and Phoxinellus because the taxonomic status of some species belonging to these genera is dubious and they could be placed in the genus Telestes. The study includes 18 species, 43 populations, and 111 individuals from 9 of the 14 peri-Mediterranean ichthyogeographic districts. Clades recovered from the phylogenetic analyses do not support previous taxonomic assumptions based on morphology. Telestes, Leuciscus, and Phoxinellus do not form monophyletic assemblages; phylogenetic analyses suggest that L. polylepis, L. turskyi, P. croaticus, and P. metohiensis should be included in Telestes. Similarly, populations of Scardinius erythrophthalmus do not cluster together and the endangered S. scardafa, endemic to central Italy and surviving in a single locality, is nested within them. The radiations of Telestes and Scardinius occurred in different time periods. A major diversification of Telestes is consistent with a sea dispersal during the freshwater Messinian "Lago Mare" phase of the Mediterranean Sea. Cladogenetic events within Scardinius are likely related to the extension and confluence of river drainages in lowlands following multiple lowering of the sea level during the Quaternary glaciations.     

Extensive mtDNA variation within the yellow-pine chipmunk,Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America

The yellow-pine chipmunk, Tamias amoenus, is common in xerophytic forests throughout much of northwest North America. We analyzed cytochrome b sequence variation from 155 individuals representing 57 localities across the distribution of T. amoenus including 10 additional species of Tamias. Maximum likelihood and parsimony tree estimation methods were used in conjunction with nested clade analysis to infer both deep and population-level processes. Our results indicate that two currently recognized subspecies of T. amoenus (T. a. canicaudus and T. a. cratericus) are not nested within other samples of T. amoenus. Maximum uncorrected levels of intraspecific sequence divergence within remaining samples of T. amoenus are >7%. Substantial geographic variation is characterized by 12 well-supported clades that correspond to distinct mountain ranges, but do not necessarily follow existing subspecific taxonomy. Significant association between geography and genealogy was detected within many of these clades and can be attributed to different population-level processes including past fragmentation, recent range expansion, and isolation by distance.     

Molecular phylogeny and evolutionary history of Southeast Asian macaques forming the M. silenus group

The 12 presently recognized taxa forming the Macaca silenus group represent the most diverse lineage within the genus Macaca. The present study was set up to clarify the phylogenetic relationships of the extant members of the M. silenus group and to explain their geographical distribution patterns seen today. A combined approach involving the analysis of one paternal (TSPY) and two maternal (cyt b and 12S-16S rRNA) molecular markers enabled us to resolve the phylogenetic relationships within this lineage. Our Y chromosomal marker is not informative enough to allow detailed conclusion. Based on our mitochondrial data, however, M. pagensis, endemic to the three southern Mentawai islands (Sipora, North- and South Pagai), split off early (2.4-2.6 mya) and represents a sister clade to the macaques from the northern Mentawai island of Siberut and from those of the Southeast Asian mainland, which diverged in a radiation-like splitting event about 1.5-1.7 mya. By combining our new results with available data on behavioural as well as climate and sea level changes in Southeast Asia during the Plio- and Pleistocene, we have developed two scenarios for the evolutionary history of this primate group, which may help explain the current geographical distribution of its members.     

Mitochondrial phylogeny reveals differential modes of chromosomal evolution in the genus Tatera (Rodentia: Gerbillinae) in Africa

The African gerbils of the genus Tatera are widespread and abundant throughout sub-Saharan Africa. There is still today a certain controversy concerning the taxonomy of these rodents and very few attempts have been made to assess their systematic relationships. The present paper introduces findings based on the partial sequences of cytochrome b (495 bp) and the 16S rRNA (469 bp) mitochondrial genes of six (T. robusta, T. nigricauda, T. vicina, T. leucogaster, T. valida, and T. kempi) species together with two additional taxa. We also report the karyotypes of T. vicina and T. leucogaster. We propose that T. vicina should be considered as a valid species and show the monophyly of the robusta species group, with the exclusion of T. leucogaster. Our results show there is a different chromosomal evolutionary pattern within the two major lineages, which is recognizable through molecular phylogenetics. One is characterized by karyotype stability and the other by a considerable number of chromosomal rearrangements. The lineage divergence coincides with the formation of the East African Rift. The processes that led to the origin of the East African species seem to be related to the subsequent climatic changes, which caused cyclic contraction and expansion of the savannah biomes. Furthermore, geological activities that characterized East Africa during Plio-Pleistocene may also have contributed to lineage divergence.