Β-fibrinogen Intron Research Articles

Phylogenetic placement and life history trait imputation for Grenada DoveLeptotila wellsi

AbstractPhylogenetic analyses can be used to resolve taxonomic uncertainties and reconstruct a species’ evolutionary history. This can be combined with ecological data to predict missing life history traits which are important for creation of conservation management strategies. We investigated the evolutionary and life history of the ‘Critically Endangered’ Grenada DoveLeptotila wellsiby estimating its phylogenetic placement and using this new phylogeny to test the accuracy of phylogenetic comparative methods for estimating both documented and unknown life history traits. We extracted DNA from two Grenada Dove samples and obtained sequences from three mitochondrial markers: Cytochrome oxidase I (COI), NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b); and one nuclear marker: β-Fibrinogen intron 7 (β-FIB). We present the first genetic data obtained for the Grenada Dove. Our data identify the Grey-Chested DoveLeptotila cassiniias the species which shares both a most recent common ancestor, with an estimated divergence of approximately 2.53 million years ago, and the smallest genetic distance (P= 0.0303) with the Grenada Dove. Life history trait values for the Grenada Dove predicted from our analyses using phylogenetic imputation are: clutch size = 2 (± 0.09) eggs; clutches per year = 1.4 (± 0.81); incubation time = 14.2 (± 0.75) days; hatching weight = 3.8 g (± 1.05) and single imputation: fledging age (genus median) = 15.5 days, longevity (genus median) = 8.6 years. This study contributes novel information regarding evolutionary history and life history characteristics to inform long-term conservation actions for a ‘Critically Endangered’ species.

Genealogy of the nuclear β-fibrinogen intron 7 in Lissotriton boscai (Caudata, Salamandridae): concordance with mtDNA and implications for phylogeography and speciation

The power of phylogeographic inference resides in its ability to integrate information from multiple sources in an iterative hypothesis- testing framework. In this paper, we build upon previous mtDNA-based hypotheses about the evolutionary history of the Iberian newt Lissotriton boscai using sequences of the highly variable nuclear β-fibrinogen intron 7. In addition to the nuclear sequences, we produced new mtDNA data across the species range to delineate contact zones and test the congruence between nuclear and mitochondrial datasets at the same level of spatial organization. Through a combination of phylogenetic, phylogeographic continuous diffusion, and genetic landscape modelling analyses, we infer the evolutionary history of the species. We found notable congruence between nuclear and mtDNA datasets, which confirms deep and consistent differentiation between two major lineages that originated in the Miocene. Additionally, we found a new nuclear haplogroup with no mtDNA counterpart, roughly circumscribed to the Iberian Sistema Central mountains, and extensive areas of nuclear admixture across mtDNA lineages. We describe potential historical dispersal routes from an ancestral hypothetical refugium in the western end of the Sistema Central in central Portugal and highlight how deep phylogeographic breaks do not necessarily indicate cryptic speciation events.

Phylogenetic origin of the endemic pigeons from Madeira (Columba trocaz) and Azores Islands (Columba palumbus azorica)

This study addresses for the first time the issue of pigeon (genus Columba) phylogeny within the archipelagos of Madeira (Columba trocaz) and Azores (C. palumbus azorica), located in the singular biogeographic area of Macaronesia. The phylogeny of these endemic pigeons was inferred based on mitochondrial (cytochrome b and cytochrome c oxidase I) and nuclear (β-fibrinogen intron 7) genetic markers through multiple approaches. Despite the non-monophyletic pattern for the insular endemic species recovered in the phylogenies, topology tests presented somewhat different results. C. trocaz, the Madeiran endemic species, clustered strongly with the Canarian endemic C. bollii, and these two are thus more closely related to each other than C. bollii to C. junoniae, the other endemic species of Canary Islands, which seems to have diverged independently. Moreover, C. trocaz was found to be phylogenetically closer to C. bollii than to C. palumbus from mainland Europe and Azores Islands. No genetic differentiation was found between the continental C. p. palumbus and the endemic C. p. azorica, which suggests a relatively recent colonisation event of the Azores Islands.

A molecular phylogeny of the eastern group of ocellated lizard genus Timon (Sauria: Lacertidae) based on mitochondrial and nuclear DNA sequences

Timon, a small genus of lacertid lizards, includes four species distributed in two separate ranges in the western and eastern part of the Mediterranean Basin. Phylogenetic relationships between the two groups have not been resolved, and the taxonomic situation of the two subspecies of the eastern representative of the genus, Timon princeps, is not clear. To address these questions, partial DNA sequences of two nuclear (β-fibrinogen intron 7 and C-mos) and three mitochondrial (cytochrome b, 12S rRNA and 16S rRNA) genes were analyzed. Based on the high genetic distance between the two subspecies of T. princeps we promote their taxonomic status to full species, Timon princeps and Timon kurdistanicus. Divergence time estimates based on other lacertid species suggest that the separation of the green (Lacerta) and ocellated (Timon) lizards took place around 12 My ago, and that the Eastern group underwent speciation around 4-5 my ago, perhaps associated with the uplifting of the Zagros mountains. As expected given this ancient divergence and complex paleogeography, considerable levels of genetic diversity are recovered within both taxa, with geographically close individuals showing very divergent haplotypes.

Mitochondrial and nuclear DNA phylogenies reveal a complex evolutionary history in the Australasian robins (Passeriformes: Petroicidae)

The Australasian robins (Petroicidae) comprise a relatively homogeneous group of small to medium-sized insectivorous birds. Their center of diversity is Australia and New Guinea (40 species) but seven species have managed to colonize geographically distant islands such as Tanimbar, New Britain, New Zealand, New Caledonia, Norfolk Island, Vanuatu, Solomon Islands, Fiji and Samoa. To resolve the evolutionary relationships within the Petroicidae, we here present the results of a phylogenetic analysis of sequence data from two mitochondrial genes (ND2, CO1) and one nuclear intron (β-Fibrinogen intron 5) for all 14 genera and 40 of the 46 currently recognized species. All phylogenetic analyses identified six primary lineages, treated here as subfamilies, within the Petroicidae: (1) Eopsaltriinae comprising Eopsaltria (excluding E. flaviventris), Tregellasia, Peneothello, Melanodryas, Poecilodryas and Heteromyias; (2) Drymodinae comprising Drymodes; (3) Microecinae comprising Microeca, Monachella and Eopsaltria flaviventris; (4) Petroicinae comprising Petroica and Eugerygone; (5) Pachycephalopsinae comprising Pachycephalopsis; and (6) Amalocichlinae comprising Amalocichla. The genera Eopsaltria, Microeca, Peneothello and Poecilodryas were found to be paraphyletic. Based on assessments of phylogenetic branching patterns and/or DNA divergence it also was apparent that Eopsaltriaaustralis, Tregellasialeucops, Melanodryascucullata, Heteromyiasalbispecularis, Drymodessupercilious and Microecaflavigaster may each comprise more than one species. The Petroicidae display a complex biogeographical history involving repeated radiations both within, and across Australia and New Guinea. It appears that dispersal into smaller islands such as New Britain, Tanimbar and the South Pacific has only been undertaken by species with a “flycatcher” body form.

A genetic characterization of European Woodcock (Scolopax rusticola, Charadriidae, Charadriiformes) overwintering in Italy

Overwintering and stop-over areas of long-distance migrants need to be identified and studied to ensure effective year-round protection measures. Here, genetic and biogeochemical markers were used to describe the structure and to infer the origin of Italian overwintering stocks of Eurasian Woodcock (Scolopax rusticola, Charadridae, Charadriiformes). A 771 base pairs fragment of mitochondrial cytochrome b gene was analyzed in 260 specimens sampled in Italy and in Scotland, Croatia, Bulgaria, Hungary and Greece. In addition, nuclear β-Fibrinogen Intron 7 gene (898 base pairs) was analyzed in a subset of 34 samples. Hydrogen/deuterium isotopic ratio was measured in 29 individuals and compared with a map of isotopic values of European rainfalls. The mitochondrial DNA analysis revealed the presence of two different haplogroups in the analyzed sample, occurring sympatrically in many sampling sites. Conversely, nuclear DNA did not show a similar pattern of differentiation. Analysis of synonymous/non-synonymous substitutions ratio in cytochrome b data set revealed a striking difference between the two disclosed haplogroups, suggesting the existence of two diverging evolutionary lineages. Genetic traces of demographic expansions were revealed for both mitochondrial lineages. Isotopic data did not suggest a clear separation of the two mtDNA haplogroups in the source breeding range but hinted at the presence of a migration pattern from the north-easternmost portion of the breeding range to the southernmost one of the wintering range. Overall, we proved the existence of two different mitochondrial lineages in the Italian overwintering stock, as well as in the other European winter samples, both characterized by a demographic increase in the recent past. Our results can be considered a valid tool to study migratory connectivity in this species, in comparison with the increasing availability of genetic data from the breeding range.

A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds

1. Methods that assess patterns of phylogenetic relatedness, as well as character distribution and evolution, allow one to infer the ecological processes involved in community assembly. Assuming niche conservatism, assemblages should shift from phylogenetic clustering to evenness with decreasing geographic scale because the relative importance of mechanisms that shape assemblages is hypothesized to be scale-dependent. Whereas habitat filtering is more likely to act at regional scales because of increased habitat heterogeneity that allows sorting of ecologically similar species in contrasting environments, competition is more likely to act at local scales because low habitat heterogeneity provides few opportunities for niche partitioning. 2. We used species lists to assess assemblage composition, data on ecologically-relevant traits, and a molecular phylogeny, to examine the phylogenetic structure of antbird (Thamnophilidae) assemblages at three different geographical scales: regional (ecoregions), intermediate (100-ha plots) and local (mixed-flocks). In addition, we used patterns of phylogenetic beta diversity and beta diversity to separate the factors that structure antbird assemblages at regional scales. 3. Contrary to previous findings, we found a shift from phylogenetic evenness to clustering with decreasing geographical scale. We argue that this does not reject the hypothesis that habitat filtering is the predominant force in regional community assembly, because analyses of trait evolution and structure indicated a lack of niche conservatism in antbirds. 4. In some cases, phylogenetic evenness at regional scales can be an effect of historical biogeographic processes instead of niche-based processes. However, regional patterns of beta diversity and phylogenetic beta diversity suggested that phylogenetic structure in our study cannot be explained by the history of speciation and dispersal of antbirds, further supporting the habitat-filtering hypothesis. 5. Our analyses suggested that competitive interactions might not play an important role locally, which would provide a plausible explanation for the high alpha diversity of antbirds in Amazonia. 6. Finally, we emphasize the importance of including trait information in studies of phylogenetic community structure to adequately assess the mechanisms that determine species co-existence.

Genetic diversity and differentiation of three Brazilian populations of Scarlet ibis (Eudocimus ruber)

The possible origin of the Scarlet ibis population of Cubatao in southern Brazil, and its levels of genetic diversity and differentiation in relation to populations from the country’s northern coast were investigated through the sequences of 980 base pairs of β-fibrinogen intron 7 from a sample of 37 specimens. A total of 19 haplotypes were recorded in the three populations. Despite observed discrepancies in the levels of genetic diversity (π = 0.0017–0.0033; h = 0.60–0.95), AMOVA, K*st and Fst values all indicated that genetic differentiation among the populations was relatively low. This suggests that the Cubatao population was isolated recently from the panmictic population that was once distributed all along the Brazilian coast, although it does not totally refute its possible derivation from a specific population on the north coast. Given our results, genetic management should focus on the minimization of inbreeding, especially in the smaller populations, such as Cubatao. However, a more definitive study, including markers with higher evolutionary rates (e.g. microsatellites) and a much larger sample, would be required before any such actions can be taken.

Molecular phylogeny of the Herpestidae (Mammalia, Carnivora) with a special emphasis on the Asian Herpestes

Until now, phylogenetic studies of the mongooses (Carnivora, Herpestidae) have not included an exhaustive sampling of the Asian members of this family. In this study, we used mitochondrial (Cytochrome b and ND2), nuclear (β-fibrinogen intron 7 and Transthyretin intron 1) sequences from almost all of the recognized mongoose species to produce a well-resolved phylogeny of the Herpestidae. We also performed molecular dating analyses to infer divergence dates of the different lineages within the Herpestidae. Our results confirmed the paraphyly of the Herpestes genus and other phylogenetic relationships, which previously had only been moderately supported. The Asian herpestid species were found to form a monophyletic group within the Herpestidae. Within the Asian species, a cyto-nuclear conflict was discovered between the small Indian mongoose ( Herpestes auropunctatus), the Indian gray mongoose ( Herpestes edwardsii) and the Javan mongoose ( Herpestes javanicus), which may have occurred through interspecific hybridization. This study inferred an Early Miocene origin for the Herpestidae and a Middle Miocene origin for the Asian mongooses.

DNA Sequence assessment of phylogenetic relationships among New World martins (Hirundinidae: Progne)

The classification of New World martins (Progne) has a convoluted history because taxonomists have relied on plumage traits that vary continuously across populations. We estimated the phylogeny of Progne by analyzing mitochondrial cytochrome b DNA sequences of 27 individuals of eight of the nine species (10 subspecies) and nuclear β-fibrinogen intron 7 sequences of 20 individuals of six species (8 subspecies). The Brown-chested Martin (P. tapera) is sister to other Progne species. The Middle American taxa—Sinaloa Martin (P. sinaloae), Cuban Martin (P. cryptoleuca), Caribbean Martin (P. dominicensis), and Central American populations of Gray-breasted Martin (P. chalybea)—form a well supported clade. This group is distinct from Purple Martin (P. subis), which has no particularly close relatives. All four Middle American taxa appear to be good species, although Cuban and Caribbean martins could be merged in view of their similar plumage and low genetic divergence (1.2%). Two of the South American taxa, the Peruvian Martin (P. murphyi) and Southern Martin (P. elegans), are also distinct species. We did not examine the Galapagos Martin (P. modesta) for lack of DNA, but it is likely to be a good species as well. An unexpected result of the study was that Gray-breasted Martin appears polyphyletic; its South American populations are closer to the Southern Martin than to its Central American populations.

Documenting the advantages and limitations of different classes of molecular markers in a well-established phylogeographic context: lessons from the Iberian endemic Golden-striped salamander, Chioglossa lusitanica (Caudata: Salamandridae)

Previous analyses of mitochondrial (mt)DNA and allozymes covering the range of the Iberian endemic golden-striped salamander, Chioglossa lusitanica, suggested a Pleistocene split of the historical species distribution into two population units (north and south of the Mondego river), postglacial expansion into the northernmost extant range, and secondary contact with neutral diffusion of genes close to the Mondego river. We extended analysis of molecular variation over the species range using seven microsatellite loci and the nuclear β-fibrinogen intron 7 (β-fibint7). Both microsatellites and β-fibint7 showed moderate to high levels of population structure, concordant with patterns detected with mtDNA and allozymes; and a general pattern of isolation-by-distance, contrasting the marked differentiation of two population groups suggested by mtDNA and allozymes. Bayesian multilocus analyses showed contrasting results as populations north and south of the Douro river were clearly differentiated based on microsatellites, whereas allozymes revealed differentiation north and south of the Mondego river. Additionally, decreased microsatellite variability in the north supported the hypothesis of postglacial colonization of this region. The well-documented evolutionary history of C. lusitanica provides an excellent framework within which the advantages and limitations of different classes of markers can be evaluated in defining patterns of population substructure and inferring evolutionary processes across distinct spatio-temporal scales. The present study serves as a cautionary note for investigations that rely on a single type of molecular marker, especially when the organism under study exhibits a widespread distribution and complex natural history. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 371–387.

Phylogenetic relationships within Passerida (Aves: Passeriformes): A review and a new molecular phylogeny based on three nuclear intron markers

The avian clade Passerida was first identified based on DNA–DNA hybridization data [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Monophyly of the Passerida, with the exception of a few taxa, has later been corroborated in several studies; however, the basal phylogenetic relationships have remained poorly understood. In this paper, we review the current knowledge of the phylogenetic relationships within Passerida and present a new phylogeny based on three nuclear introns (myoglobin intron 2, ornithine decarboxylase introns 6 and 7, as well as β-fibrinogen intron 5). Our findings corroborate recent molecular hypotheses, but also identify several hitherto unrecognized relationships.

Phylogenetic relationships of the Asian palm civets (Hemigalinae & Paradoxurinae, Viverridae, Carnivora)

The Viverridae (Mammalia, Carnivora), one of the least studied groups of carnivorans, include two subfamilies of Asian palm civets: Hemigalinae and Paradoxurinae. The relationships between and within these two subfamilies have never been thoroughly tested using an extensive molecular sample set. In this study, we gathered sequences of four genes (two mitochondrial: Cytochrome b and ND2 and two nuclear: β-fibrinogen intron 7 and IRBP exon 1) for eight of the eleven extant species representing these two subfamilies. The results showed that: (1) the Asian palm civets (Hemigalinae and Paradoxurinae) have a single origin and form the sister-group of the (Genettinae+Viverrinae) clade, (2) the Hemigalinae (including the otter civet Cynogale bennettii) are monophyletic, (3) the Paradoxurinae are monophyletic and (4) the small-toothed palm civet (Arctogalidia trivirgata) is an early offshoot within the Paradoxurinae. Using a relaxed molecular clock analysis, the differentiation of the (Hemigalinae+Paradoxurinae) was inferred to occur in the Late Oligocene/Early Miocene.

β-fibrinogen intron 7 variation in Discoglossus (Anura: Discoglossidae): implications for the taxonomic assessment of morphologically cryptic species

AbstractThe generalized use of nuclear introns in combination with mitochondrial DNA data in molecular systematic and intraspecific phylogeographical studies is providing new insights into the complex evolutionary histories of taxa surviving the Quaternary glaciations. Previous studies have highlighted the suitability of the beta-fibrinogen intron 7 (β-fibint7) for phylogenetic and phylogeographic studies in a wide variety of taxa, including amphibians. Here we use sequences of this marker to assess inter- and intraspecific variation in Discoglossus (Discoglossidae), with special emphasis on geographic patterns of genetic structure in the Iberian Peninsula, where recent studies have questioned the taxonomic status of D. jeanneae. We obtained 81 sequences of β-fibint7 from samples including all currently recognized species except D. montalentii and 37 populations in the Iberian Peninsula and compared levels of genetic variation with those observed in a fragment of similar length of the mtDNA gene cytochrome b. The sequence of β-fibint7 in Discoglossus is the shortest described for amphibians so far, 378 base pairs. In general, we found low levels of variability (only 26 parsimony-informative sites in the dataset), with no alternatively fixed haplotypes in samples attributed to D. galganoi or D. jeanneae based on their mtDNA. Values of pairwise sequence divergence between non-Iberian species ranged from 1.1% to 4.5% (13.3% to 20.9% in mtDNA). The patterns observed in samples from the Iberian Peninsula are consistent with either incomplete lineage sorting or ongoing gene flow between D. galganoi and D. jeanneae. We conclude by reviewing the genetic evidence available to address the taxonomic status of Iberian species of Discoglossus.

Evolutionary history of woodpeckers and allies (Aves: Picidae): Placing key taxa on the phylogenetic tree

We analyzed 2995 base pairs of nucleotide sequence data (nuclear β-fibrinogen intron 7 and mitochondrial cytochrome b and ND2 genes), using parsimony and model-based approaches to infer phylogenetic relationships of the woodpeckers and allies, yielding novel hypotheses for several critical gaps in the knowledge of picid phylogeny. We tested the monophyly of sub-families within the Picidae, and sampled from widely distributed and diverse genera ( Celeus, Colaptes, Dryocopus, Melanerpes, Picoides, Picumnus, Sasia, Piculus, and Picus). Relationships of three poorly known Southeast Asian genera ( Dinopium, Reinwardtipicus, and Blythipicus) were also examined, revealing unexpected sister relationships. All phylogenetic approaches recovered largely congruent topologies, supporting a monophyletic Picinae and paraphyletic Picumninae, with the monotypic piculet, Nesoctites micromegas, as sister to the Picinae. We report paraphyly for Celeus and Piculus, whereas the broadly distributed genera Picumnus and Dryocopus were supported as monophyletic. Our phylogenetic results indicate a complex geographic history for the Picidae, with multiple disjunct sister lineages distributed between the New World and Asia. The relationships and geographic distribution of basal picid lineages indicates an Old World origin of the Picidae; however, the geographic origin of the Picinae remains equivocal, as the sister relationship between the Caribbean N. micromegas and the true woodpeckers presents the possibility of a New World origin for the Picinae.

Phylogenetic relationships amongst swifts and swiftlets: A multi locus approach

We recently reconstructed the troublesome swiftlet phylogeny using cytochrome- b mitochondrial DNA sequences. The relationship of the giant swiftlet ( Hydrochous gigas) with swiftlets of the genus Aerodramus was, however, unresolved. In an attempt to clarify this issue, we now incorporated mitochondrial 12S rRNA and nuclear β-fibrinogen intron 7 nuclear DNA sequences with the cyt- b sequences of six swiftlet, two swift, and one hummingbird outgroup species. A partition homogeneity (PH) test, used to determine the congruence of phylogenetic signal between two sets of sequences, suggested that cyt- b and Fib7 sequences were incongruent and therefore should not be combined. However, further analyses revealed that the apparent incongruence was probably due to the high amount of variation in cyt- b sequences. Separate and combined analyses of the three sequences unambiguously placed H. gigas as the sister-group of Aerodramus and supported monophyly of the swiftlets. These results were supported by analyses of combined NADH dehydrogenase subunit-2 (ND2) and cyt- b sequences of H. gigas in combination with sequences previously published by other workers. Recently, it was shown that the pygmy swiftlet ( C. troglodytes)—in our phylogenetic analyses consistently placed with other, non-echolocating, Collocalia species—is in fact able to echolocate. Echolocation thereby lost its value to distinguish between different swiftlet genera. Furthermore, the phylogenetic distribution of echolocation can be explained either by its single evolution at the base of the swiftlets, with subsequent loss, or by independent evolution in Aerodramus and C. troglodytes. Because yet unpublished data suggest that only the auditory nuclei in swiftlet brains show adaptations to echolocation, the latter explanation seems the more likely one.

Phylogeny of eagles, Old World vultures, and other Accipitridae based on nuclear and mitochondrial DNA

We assessed phylogenetic relationships for birds of prey in the family Accipitridae using molecular sequence from two mitochondrial genes (1047 bases ND2 and 1041 bases cyt- b) and one nuclear intron (1074 bases β-fibrinogen intron 7). We sampled representatives of all 14 Accipitridae subfamilies, focusing on four subfamilies of eagles (booted eagles, sea eagles, harpy eagles, and snake eagles) and two subfamilies of Old World vultures (Gypaetinae and Aegypiinae) with nearly all known species represented. Multiple well-supported relationships among accipitrids identified with DNA differ from those traditionally recognized based on morphology or life history traits. Monophyly of sea eagles (Haliaeetinae) and booted eagles (Aquilinae) was supported; however, harpy eagles (Harpiinae), snake eagles (Circaetinae), and Old World vultures were found to be non-monophyletic. The Gymnogene ( Polyboroides typus) and the Crane Hawk ( Geranospiza caerulescens) were not found to be close relatives, presenting an example of convergent evolution for specialized limb morphology enabling predation on cavity nesting species. Investigation of named subspecies within Hieraaetus fasciatus and H. morphnoides revealed significant genetic differentiation or non-monophyly supporting recognition of H. spilogaster and H. weiskei as distinctive species.

Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear β-fibrinogen intron 7 to carnivores

The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear β-fibrinogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; ≈3750 bp) and combined mt and nuclear data (nine genes; ≈6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manul within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear β-fibrinogen intron 7.

Phylogeny of swallows (Aves: Hirundinidae) estimated from nuclear and mitochondrial DNA sequences

The phylogeny of swallows was reconstructed by comparing segments of three genes, nuclear β-fibrinogen intron 7 (βfib7), mitochondrial cytochrome b (cytb), and mitochondrial ND2, in a variety of combinations using maximum likelihood and Bayesian methods. βfib7 was sequenced for 47 species, cytb for 74 species, and ND2 for 61 species to yield comparisons among 75 of the 84 currently recognized swallow species. The family Hirundinidae was confirmed to consist of two clades, Pseudochelidoninae (river martins) and Hirundininae (typical swallows). The Hirundininae is further divided into mud nesters ( Hirundo sensu lato), core martins ( Phedina, Riparia, and New World endemic genera), and basal relicts ( Psalidoprocne, Cheramoeca, and Pseudhirundo). We did not resolve the hierarchy among these three hirundinine groups, but discovered many relationships within them. Mud-nesting genera have the following relationships: ( Hirundo sensu stricto, Ptyonoprogne), ( Delichon, ( Petrochelidon, Cecropis)). Core martins have the following topology: ( Phedina, Riparia cincta), ( Riparia sensu stricto, Tachycineta, (( Stelgidopteryx, Progne), (Neotropical endemic genera))). Interspecific relationships among the Neotropical endemics were resolved completely; Atticora and Notiochelidon are paraphyletic, and all Neotropical endemics probably should be lumped into one or two genera. The final group of hirundinines, the basal relicts, consists of a sister pair, the Australian Cheramoeca and African Pseudhirundo. The African saw-wings ( Psalidoprocne) are their likely sister group.

Phylogeny and evolution of the green lizards, Lacerta spp. (Squamata: Lacertidae) based on mitochondrial and nuclear DNA sequences

AbstractPartial DNA sequences from three mitochondrial (cytochrome b, 12S rRNA and 16S rRNA) and two nuclear (β-fibrinogen intron 7 and C-mos) genes were used to estimate the phylogenetic relationships among all eight extant species of green lizards, Lacerta sensu stricto, and many currently recognized subspecies. All eight species form a monophyletic group. L. agilis, L. schreiberi and L. strigata are genetically well differentiated species. L. trilineata and L. pamphylica are not monophyletic units based on analyses of the β-fibrinogen intron 7. Lacerta media is closely related to some Lacerta trilineata. L. bilineata and L. viridis are closely related, and recognition of L. bilineata as a distinct species makes L. viridis paraphyletic also. For both L. bilineata and L. viridis, some subspecies appear to remain in their southern glacial refugia, while a single genetic entity shows successfully postglacial expansion. The topology derived from C-mos variation is concordant with that derived from mtDNA, with substitutions occurring at a similar rate to that of transversions in the rRNA genes. Although C-mos is typically used at deeper taxonomic levels it is also phylogenetically informative within green lizards. β-fibrinogen intron 7, typically used for assessing phylogenetic relationships among bird species, is a useful phylogenetic marker for reptiles also, showing considerable variation between species. There is not complete concordance between estimates of relationships derived from the mtDNA and nuclear markers, probably because rapid diversification led to incomplete lineage sorting in the green lizards. Introgression could also be occuring between some species.