Alignment and phylogenetic analysis of beta-fibrinogen intron 7 sequences among avian orders reveal conserved regions within the intron

We sequenced beta-fibrinogen intron 7 (beta-fibint 7) from 28 species of birds, representing 18 families in nine orders. Although the antiquity of the avian orders is estimated to be 55 to 90 Myr, and numerous indels have accrued among diverging lineages, the intron sequences were not difficult to align. However, alignment of avian sequences with mammal or snake sequences was difficult, and the residual phylogenetic signal was weak. beta-fibint 7 is an AT-rich intron, and its base composition varies little over the diversity of birds represented by our sample. Alignment of these anciently diverged sequences reveals at least five clusters of conserved nucleotides; at least two clusters appear to be in excess of the minimal set usually associated with intron excision, but their functions are unknown. Two equally most-parsimonious (MP) trees were found when indels were not included in the phylogenetic analysis, and six such trees were found when indels were included. The Neighbor-Joining and maximum-likelihood trees were identical to each other and to one of the MP trees in each MP analysis. Indels, as well as nucleotide substitutions, are phylogenetically informative, and bootstrap support exceeded 90% for 21 of 24 inferred nodes when indels were included in the MP analysis. All traditional orders represented by two or more species appear monophyletic. Relationships among avian orders are strongly supported with the exception of an inferred sister-group relationship between Caprimulgiformes and Columbiformes. A relatively close relationship between Piciformes and Passeriformes is inferred, at odds with earlier DNA-DNA hybridization studies but consistent with traditional classifications. Among Passeriformes, the traditional perspective of a sister-group relationship of suboscines and oscines is supported, as is the subsequent split of the oscines into a lineage representative of the Corvida before the diversification of the Passerida. The four species of owls divide into two strongly supported clades, corresponding to the widely accepted bifurcation of owls into two families, Tytonidae and Strigidae. A sister-group relationship between gallinaceous birds and waterfowl, the Galloanserae, is also strongly supported.     

Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)

Insertion and deletion events (indels) provide a suite of markers with enormous potential for molecular phylogenetics. Using many more indel characters than those in previous studies, we here for the first time address the impact of indel inclusion on the phylogenetic inferences of Arctoidea (Mammalia: Carnivora). Based on 6843 indel characters from 22 nuclear intron loci of 16 species of Arctoidea, our analyses demonstrate that when the indels were not taken into consideration, the monophyly of Ursidae and Pinnipedia tree and the monophyly of Pinnipedia and Musteloidea tree were both recovered, whereas inclusion of indels by using three different indel coding schemes give identical phylogenetic tree topologies supporting the monophyly of Ursidae and Pinnipedia. Our work brings new perspectives on the previously controversial placements among Arctoidea families, and provides another example demonstrating the importance of identifying and incorporating indels in the phylogenetic analyses of introns. In addition, comparison of indel incorporation methods revealed that the three indel coding methods are all advantageous over treating indels as missing data, given that incorporating indels produces consistent results across methods. This is the first report of the impact of different indel coding schemes on phylogenetic reconstruction at the family level in Carnivora, which indicates that indels should be taken into account in the future phylogenetic analyses.     

Phylogeny of the caniform carnivora: evidence from multiple genes

The monophyletic group Caniformia in the order Carnivora currently comprises seven families whose relationships remain contentious. The phylogenetic positions of the two panda species within the Caniformia have also been evolutionary puzzles over the past decades, especially for Ailurus fulgens (the red panda). Here, new nuclear sequences from two introns of the β-fibrinogen gene (β-fibrinogen introns 4 and 7) and a complete mitochondrial (mt) gene (ND2) from 17 caniform representatives were explored for their utilities in resolving higher-level relationships in the Caniformia. In addition, two previously available nuclear (IRBP exon 1 and TTR intron 1) data sets were also combined and analyzed simultaneously with the newly obtained sequence data in this study. Combined analyses of four nuclear and one mt genes (4417 bp) recover a branching order in which almost all nodes were strongly supported. The present analyses provide evidence in favor of Ailurus fulgens as the closest taxon to the procyonid-mustelid (i.e., Musteloidea sensu stricto) clade, followed by pinnipeds (i.e., Otariidae and Phocidae), Ursidae (including Ailuropoda melanoleuca), and Canidae, the most basal lineage in the Caniformia. The potential utilities of different genes in the context of caniform phylogeny were also evaluated, with special attention to the previously unexplored β-fibrinogen intron 4 and 7 genes.     

Phylogenetic analysis of the Malvadendrina clade (Malvaceae s.l.) based on plastid DNA sequences

Phylogenetic relationships within Malvaceae s.l., a clade that includes the traditional families Bombacaceae, Malvaceae s.str., Sterculiaceae, and Tiliaceae, have become greatly clarified thanks to recent molecular systematic research. In this paper, we use DNA sequences of four plastid regions (atpB, matK, ndhF, and rbcL) to study relationships within Malvadendrina, one of the two major clades of Malvaceae s.l. The four data sets were generally in agreement, but five terminal taxa manifested highly unexpected affinities in the rbcL partition, and the non-coding sequences of the trnK intron were found to provide limited phylogenetic information for resolving relationships at the base of Malvadendrina. The remaining data strongly support the existence of six major clades within Malvadendrina: Brownlowioideae, Dombeyoideae, Helicteroideae, Malvatheca (comprising Bombacoideae and Malvoideae), Sterculioideae, and Tilioideae. These data also resolve the placement of two problematic taxa: Nesogordonia (in Dombeyoideae) and Mortoniodendron (in Tilioideae). The relationships among the six clades are not definitively resolved, but the best-supported topology has Dombeyoideae as sister to the remainder of Malvadendrina (posterior probability PP=80%) and Sterculioideae as sister to Malvatheca (PP=86%). This early branching position of Dombeyoideae is supported by similarities in floral characters between members of that clade and outgroup taxa in Byttnerioideae. Similarly, the sister-group relationship of Sterculioideae and Malvatheca receives support from androecial characteristics, like subsessile or sessile anthers and an absence of staminodes, shared by these two clades.     

Exhaustive sample set among Viverridae reveals the sister-group of felids: the linsangs as a case of extreme morphological convergence within Feliformia

Although molecular studies have helped to clarify the phylogeny of the problematic family Viverridae, a recent phylogenetic investigation based on cytochrome b (cyt b) has excluded the Asiatic linsangs (genus Prionodon) from the family. To assess the phylogenetic position of the Asiatic linsangs within the Feliformia, we analysed an exhaustive taxonomic sample set with cyt b and newly produced transthyretin intron I sequences (TR-I-I). TR-I-I alone and cyt b +TR-I-I combined (maximum-likelihood analysis) highly support the position of Asiatic linsangs as sister-group of the Felidae. The estimation of minimum divergence dates from molecular data suggests a splitting event ca. 33.3 million years (Myr) ago, which lends support to historical assertions that the Asiatic linsangs are "living fossils" that share a plesiomorphic morphotype with the Oligocene feliform Paleoprionodon. The African linsang is estimated to appear more than 20 Myr later and represents the sister-group of the genus Genetta. Our phylogenetic results illustrate numerous morphological convergences of "diagnostic" characters among Feliformia that might be problematic for the identification of fossil taxa. The morphotype reappearance from the Asiatic to the African linsangs suggests that the genome of the Feliformia conserved its potential ability of expression for a peculiar adaptive phenotype throughout evolution, in this case arboreality and hypercarnivory in tropical forest.     

Caryophyllales: Evaluating phylogenetic signal in trnK intron versus matK

Abstract We assess the phylogenetic information in trnK intron at the ordinal level using the Caryophyllales and compare it with that derived from matK. The trnK gene is split into two exons by an intron that includes the matK gene. The plastid trnK is a tRNA gene encoding Lysine^(UUU), whereas the matK gene is a putative group II intron maturase. The two regions are usually coamplified, and trnK intron is partially sequenced but its sequences are often excluded from phylogenetic reconstruction at deep historic levels. This study shows that the two regions are comparable in proportion of variable sites, possess a comparable pattern of substitution rates per site, and display similar phylogenetic informativeness profiles and per‐site informativeness. Phylogenetic analyses show strong congruence between phylogenetic trees based on matK and trnK intron partitioned datasets from 45 genera representing 30 of the 34 recognized Caryophyllales families. The trnK intron alone provides a relatively well‐resolved topology for the order. Combining the trnK intron with matK sequence data resulted in six most parsimonious trees, differing only in the placement of Claytonia (Portulacaceae) within the noncore group. A well‐supported major basal split in the order into core and noncore Caryophyllales with Rhabdodendraceae, Simmondsiaceae, and Asteropeiaceae as sister to remaining core lineages is evident in partitioned and combined analyses. The placement of these three families has been disputable, impacting the overall backbone topology of the Caryophyllales. This study demonstrates the cost effectiveness of using the trnK intron along with matK (both substitutions and insertions/deletions) at deeper phylogenetic level.     

Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes

Phylogenetic relationships among 37 living species of order Carnivora spanning a relatively broad range of divergence times and taxonomic levels were examined using nuclear sequence data from exon 1 of the IRBP gene (approximately 1.3 kb) and first intron of the TTR gene (approximately 1 kb). These data were used to analyze carnivoran phylogeny at the family and generic level as well as the interspecific relationships within recently derived Felidae. Phylogenetic results using a combined IRBP+TTR dataset strongly supported within the superfamily Califormia, the red panda as the closest lineage to procyonid-mustelid (i.e., Musteloidea) clade followed by pinnipeds (Otariidae and Phocidae), Ursidae (including the giant panda), and Canidae. Four feliform families, namely the monophyletic Herpestidae, Hyaenidae, and Felidae, as well as the paraphyletic Viverridae were consistently recovered convincingly. The utilities of these two gene segments for the phylogenetic analyses were extensively explored and both were found to be fairly informative for higher-group associations within the order Carnivora, but not for those of low level divergence at the species level. Therefore, there is a need to find additional genetic markers with more rapid mutation rates that would be diagnostic at deciphering relatively recent relationships within the Carnivora.     

Removal of Noisy Characters from Chloroplast Genome-Scale Data Suggests Revision of Phylogenetic Placements of <Emphasis Type="Italic">Amborella</Emphasis> and <Emphasis Type="Italic">Ceratophyllum</Emphasis>

It is widely appreciated that noisy, highly variable data can impede phylogeney reconstruction. Researchers have for a long time omitted problematic data from phylogenetic analyses, such as the third-codon positions and variable regions. In the analyses of the phylogenetic relations of the angiosperms; however, inclusion of complete gene sequences into genomic-scale alignments has become a common practice. Here we demonstrate that this practice can be misleading. We show that support of the basal-most position of Amborella trichopoda among the angiosperms in the chloroplast genomic data is based only on a tiny subset (< 1% of the total alignment length) of the most variable positions in alignment, exhibiting mean maximum likelihood (ML) distance among the angiosperm operational taxonomic units (OTUs) approximately 36 substitutions/site. Exclusion of these positions leads to disappearance of the basal Amborella branch. Likewise, the recently reported sister-group relationship of Ceratophyllum to the eudicots is based on the presence of 2% of the most variable positions in the genomic alignment, exhibiting, on average, 20 substitutions/site in comparison among the angiosperm OTUs. These observations highlight a need for excluding a certain proportion of saturated positions in alignment from phylogenomic analyses.     

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.     

Tempo and mode of evolution in an orthologous Can SINE

Tempo and mode of nucleotide change were examined in an orthologous carnivoran nuclear repetitive DNA element (Can SINE), and compared with those of the transthyretin intron I (TR-i-I) sequence in which it is embedded, by using a phylogenetic framework. The Can SINE is found in representatives of all living caniform carnivoran families, but no living feliform families. This suggests insertion 40–65 MYA, after the two lineages split, but before the caniform radiation. Despite linkage and a long shared evolutionary history, both parsimony and likelihood analyses showed the Can SINE to be significantly different from TR-i-I in rates of evolution and phylogenetic hypotheses supported. The substitution rate is significantly higher in Can SINE than in TR-i-I, and this is attributable to the tRNA-related region of the insertion. While the incongruence length difference test revealed significant conflict between the Can SINE and TR-i-I partitions, the test was shown to be sensitive to the distribution of homoplasy within partitions. The conflicting phylogenies are likely the result of differences in phylogenetic accuracy (homoplasy distribution) rather than in phylogenetic history (gene trees). The base composition of Can SINE contains a significantly higher GC percentage than TR-i-I. Our results indicate that differences between the two partitions may be the result of homoplasy introduced by an increased substitution rate in the tRNA-related region of Can SINE owing to CpG hypermutability. Received: 21 April 2000 / Accepted: 24 August 2000     

Phylogenetic Relationships of Extinct Cetartiodactyls: Results of Simultaneous Analyses of Molecular, Morphological, and Stratigraphic Data

Although some recent morphological and molecular studies agree that Cetacea is closely related to Hippopotamidae, there is little consensus on the phylogeny within Cetartiodactyla. We addressed this problem by conducting two analyses: (1) a simultaneous cladistic analysis of intrinsic data (morphology and molecules) and (2) a stratocladistic analysis, which included morphological, molecular, and stratigraphic data. Unlike previous simultaneous analyses, we had the opportunity to include data from the recently described hindlimbs of protocetid and pakicetid cetaceans. Our intrinsic dataset includes 73 taxa scored for 8,229 informative characters, of which 208 are morphological and 8,021 molecular. Both analyses supported the exclusion of Mesonychia from Cetartiodactyla and a close phylogenetic relationship between Hippopotamidae and Cetacea. Many polytomies in the strict consensus of the most parsimonious trees for the intrinsic dataset can be attributed to differing positions for Raoellidae, which in some trees is the sister-group to Cetacea. Pruning Raoellidae and 18 other taxa from all most parsimonious produced a fully resolved agreement subtree, which indicates that the Old World taxa Cebochoerus and Mixtotherium are successive stem taxa to Whippomorpha (i.e., Cetacea + Hippopotamidae). The main result of adding stratigraphic information to the intrinsic dataset was that we found fewer most parsimonious trees, which in most respects were congruent with a subset of the shortest trees for the intrinsic dataset. Our stratocladistic analysis supports species of Diacodexis as the most basal cetartiodactyls, a clade of suiform cetartiodactyls, a monophyletic Tylopoda that includes Protoceratidae, and a monophyletic Carnivora. We were unable to identify any pre-Miocene stem taxa to Hippopotamidae, thus its ghost lineage is still 39 million years long. The relatively low Bremer support for many nodes in our trees indicates that our phylogenetic hypotheses should be subjected to further testing.     

Molecular and phylogenetic analysis of PCR-amplified cyclin-dependent kinase (CDK) family sequences from representatives of the earliest available lineages of eukaryotes

Cyclin-dependent kinase (CDK) and cell division control (CDC2) sequences are strongly conserved among eukaryotes and may complement the use of other sequence families in eukaryotic phylogenetic inference. We synthesized degenerate PCR primers to amplify the catalytic region of CDK homologs in representatives of the earliest available lineages of eukaryotes. CDK family sequence-based, maximum-likelihood distance measurements with neighbor joining, and Fitch-Margoliash least-squares analyses produced unrooted dendrograms that included protists, yeasts, and higher eukaryotes. Bootstrap confidence estimates supported CDK-based phylogenetic groupings among the protists, fungi, and vertebrates although resolution within these groups was often insignificant. However, Trichomonas vaginalis and Giardia lamblia exhibited two of the most divergent CDK-like sequences consistent with rRNA-phylogenetic inference of early divergence of these eukaryotic lineages. In the evolution from unicellular to multicellular organisms, a constellation of amino acid residues aligning with the human, CDK N-terminal sheet may have undergone abrupt replacement.Abbreviations CDC cell division control - CDK cyclin-dependent kinase family - PCR polymerase chain reaction Correspondence to: D.E. Riley     

Complete Mitochondrial DNA Sequences of Six Snakes: Phylogenetic Relationships and Molecular Evolution of Genomic Features

Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNA^Leu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences.[Reviewing Editor: Dr. Bill Ballard]     

Evolution of the primate cytochrome c oxidase subunit II gene

We examined the nucleotide and amino acid sequence variation of the cytochrome c oxidase subunit II (COII) gene from 25 primates (4 hominoids, 8 Old World monkeys, 2 New World monkeys, 2 tarsiers, 7 lemuriforms, 2 lorisiforms). Marginal support was found for three phylogenetic conclusions: (1) sister-group relationship between tarsiers and a monkey/ape clade, (2) placement of the aye-aye (Daubentonia) sister to all other strepsirhine primates, and (3) rejection of a sister-group relationship of dwarf lemurs (i.e., Cheirogaleus) with lorisiform primates. Stronger support was found for a sister-group relationship between the ring-tail lemur (Lemur catta) and the gentle lemurs (Hapalemur). In congruence with previous studies on COII, we found that the monkeys and apes have undergone a nearly two-fold increase in the rate of amino acid replacement relative to other primates. Although functionally important amino acids are generally conserved among all primates, the acceleration in amino acid replacements in higher primates is associated with increased variation in the amino terminal end of the protein. Additionally, the replacement of two carboxyl-bearing residues (glutamate and aspartate) at positions 114 and 115 may provide a partial explanation for the poor enzyme kinetics in cross-reactions between the cytochromes c and cytochrome c oxidases of higher primates and other mammals. Correspondence to: R.L. Honeycutt     

Evolution of the order Urostylida (Protozoa, Ciliophora): new hypotheses based on multi-gene information and identification of localized incongruence

Previous systematic arrangement on the ciliate order Urostylida was mainly based on morphological data and only about 20% taxa were analyzed using molecular phylogenetic analyses. In the present investigation, 22 newly sequenced species for which alpha-tubulin, SSU rRNA genes or ITS1-5.8S-ITS2 region were sampled, refer to all families within the order. Following conclusions could be drawn: (1) the order Urostylida is not monophyletic, but a core group is always present; (2) among the family Urostylidae, six of 10 sequenced genera are rejected belonging to this family; (3) the genus Epiclintes is confirmed belonging to its own taxon; (4) the family Pseudokeronopsidae undoubtedly belongs to the core portion of urostylids; however, some or most of its members should be transferred to the family Urostylidae; (5) Bergeriellidae is confirmed to be a valid family; (6) the distinction of the taxon Acaudalia is not supported; (7) the morphology-based genus Anteholosticha is extremely polyphyletic; (8) ITS2 secondary structures of Pseudoamphisiella and Psammomitra are rather different from other urostylids; (9) partition addition bootstrap alteration (PABA) result shows that bootstrap values usually tend to increase as more gene partitions are included.     

Phylogenetic Affinities Among the Extant Malagasy Lemurs (Lemuriformes) Based on Morphology and Behavior

The difficulty in achieving a consensus on the phylogenetic relationships of lemuriform primates has been due largely to the lack of a lemur fossil record and to the lack of an appropriate outgroup that would facilitate polarization of character states. Recent findings allow us to polarize some of the bony characters, but to a large extent this problem still remains. In the past, phylogenetic analyses have focused on specialized character sets such as dentition or basicranial traits, or they have employed differential weighting schemes to a more variable set of characters. In the analysis presented here, I combined all relevant characters available in the literature into one data set but restricted my selection to those traits having discontinuous states and for which no contradictory coding schemes were published. I reduced the assumptions in this analysis by removing most external weighting and ordering effects on these data sets. The available data from the literature were supplemented with data from my own observations at the Duke University Primate Center. Data were collected for 25 characters and 20 taxa and were submitted to a cladistic analysis. Some important findings from this study include support for (1) a sister-group relationship between Lepilemur and the Indridae, (2) a sister-group relationship between the Lemuridae (except Varecia) and the Indridae/Lepilemur clade, (3) a monophyletic genus Eulemur, and (4) the exclusion of Varecia from the Lemuridae.     

Hidden patterns of phylogenetic non‐stationarity overwhelm comparative analyses of niche conservatism and divergence

Aim Despite the importance of the niche concept in ecological and evolutionary theory, there are still many discussions about its definition and operational evaluation, especially when dealing with niche divergence and conservatism in an explicit phylogenetic context. Here we evaluate patterns of niche evolution in 67 New World Carnivora species, measured using Hellinger distances based on MAXENT models of species distribution. We show how inferences on niche conservatism or divergence depend on the way phylogenetic patterns are analysed using matrix comparison techniques. Innovation Initially we used the simplest approach of Mantel tests to compare Hellinger distances ( N ) derived from MAXENT and phylogenetic distances ( P ) among species. Then we extended the Mantel test to generate a multivariate correlogram, in which phylogenetic patterns are analysed at multiple levels in the phylogeny and can reveal nonlinearity in the relationship between divergence and time. Finally, we proposed a new approach to generate ‘local’ (or ‘specific’) leverages of components for Mantel correlation, evaluating the non‐stationarity in the relationship between N and P for each species. This new approach was used to show if some lineages are more prone to niche shift or conservatism than others. Main conclusions Standard Mantel tests indicated a poor correspondence between N and P matrices, discarding the idea of niche conservatism for Carnivora, but the correlogram supports that closely related species tend to be more similar than expected by chance. Moreover, the variance among Hellinger distances between pairs of closely phylogenetically related species is much larger than for the entire clade. Phylogenetic non‐stationarity analysis shows that in some Carnivora families the niche tends to divergence (Mustelidae and Canidae), whereas in others it tends to conservatism (Procyonidae and Mustelidae) at short phylogenetic distances. Our analyses clearly show that misleading results may appear if niche divergence is analysed only by simple matrix correlations not taking into account complex patterns of phylogenetic nonlinearity and non‐stationarity.     

Evolutionary history of the Paradoxurus palm civets – a new model for Asian biogeography

Aim Using molecular data and dental features, we investigated the genetic and morphological diversity among species of palm civets in the genus Paradoxurus, with a focus on the common palm civet, Paradoxurus hermaphroditus (Carnivora, Viverridae), in order to address biogeographic scenarios and provide recommendations for a taxonomic revision. Location Asia: Pakistan to the Lesser Sunda Islands. Methods We investigated the genetic diversity within Paradoxurus using two mitochondrial (cytochrome b, control region) and one nuclear (intron 7 of the β‐fibrinogen) markers. We used samples from 85 individuals of P. hermaphroditus (including 20 museum specimens) and one representative of each of the other species in the genus Paradoxurus: Paradoxurus jerdoni and Paradoxurus zeylonensis. DNA sequences were analysed using phylogenetic and haplotype network methods, and divergence dates were estimated for the clades retrieved. Furthermore, we examined dental characters from a large series of specimens and compared the morphological variation with the molecular data. Results Our phylogenetic analyses revealed that P. hermaphroditus is paraphyletic. We identified three major lineages distributed: (1) in the Indian subcontinent, south China, Hainan and in areas above 200 m in Indochina; (2) in Peninsular Malaysia, Java, Sumatra and in areas below 200 m in Indochina; and (3) in Borneo, the Philippines and the Mentawai archipelago. Our morphological observations were congruent with these three molecular lineages. Divergence date estimates inferred a Pliocene origin for Paradoxurus (2.8–5.7 Ma), with the three main clades diversifying from the mid–Early Pliocene to the end of the Pliocene. We suggest that the flooding of the Isthmus of Kra during the Pliocene was a major event shaping the diversification of Paradoxurus palm civets. We also hypothesize that the elevational segregation of the two lineages on the mainland could have resulted from the vegetational changes that were induced by Late Pliocene glacial episodes. Main conclusions The Isthmus of Kra is a major boundary between two major lineages of P. hermaphroditus. There is a need for a taxonomic revision for P. hermaphroditus, and we suggest that this species should be split into at least three species.     

FGF gene family characterization provides insights into its adaptive evolution in Carnivora

Fibroblast growth factors (FGFs) encoded by the FGF gene family can regulate development and physiology in animals. However, their evolutionary characteristics in Carnivora are largely unknown. In this study, we identified 660 sequences of three types of FGF genes from 30 unannotated genomes of Carnivora animals (before 7th May 2020), and the FGF genes from 52 Carnivora species were analyzed through the method of comparative genomics. Phylogenetic and selective pressure analyses were carried out based on the FGF genes of these 52 Carnivora species. The phylogenetic analysis results demonstrated that the FGF gene family was divided into 10 subfamilies and that FGF5 formed one clade rather than belonging to the subfamilies of FGF4 and FGF6. The evolutionary analysis results showed that the FGF genes were prominently subjected to purifying selection and were highly conserved in the process of Carnivora evolution. We also carried out phylogenetic comparative analyses, which indicated that the habitat was one of the factors that shaped the evolution of Carnivora FGF genes. The FGF1 and FGF6 genes were positively selected in the Carnivora animals, and positive selection signals were detected for the FGF19 gene in semiaquatic Carnivora animals. In summary, we clarified the phylogenetic and evolutionary characteristics of Carnivora FGF genes and provided valuable data for future studies on evolutionary characterization of Carnivora animals.