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1.
By caching acorns, jays serve as important dispersal agents for oak (Quercus) species. Yet little is known about which acorn characteristics affect selection by jays. In the traditional model of jay/oak
symbiosis, large, brown, ripe acorns free of invertebrate parasites (e.g., Curculio acorn weevils) are selected by jays. Recently, it has been suggested that a tri-trophic relationship between oaks, jays,
and weevils may have evolved to counter the negative dietary effects of acorn tannins. Under the tri-trophic model, jays would
preferentially select acorns containing weevil larvae. We tested the assumptions that (1) acorns containing curculionid larvae
exist in sufficient quantities to support jay populations and (2) jays can detect, and preferentially select, acorns containing
weevil larvae, and investigated the cues by which jays select acorns. Captive Mexican jays (Aphelocomaultramarina) were presented Emory oak (Quercusemoryi) acorns in aviary feeding trials. Large, dense, viable acorns free of curculionid larvae were preferentially selected. Contrary
to results of previous research, color did not affect selection. Acorn viability increased and curculionid larval occupancy
decreased in adjacent savannas and isolated stands relative to existing oak woodland, perhaps favoring oak recruitment into
adjacent lower-elevation grasslands. Our results compel us to reject the tri-trophic model for this system, and are consistent
with the traditional jay/oak symbiosis model. Relatively long-distance dispersal of viable acorns favors Emory oak replacement,
and spatial patterns of acorn viability and curculionid parasitism suggest expansion of Emory oak into adjacent low-elevation
semi-arid grasslands.
Received: 29 February 1996 / Accepted: 26 September 1996 相似文献
2.
White‐throated magpie‐jays (Calocitta formosa) and brown jays (Cyanocorax morio) are cooperative breeders that live in complex groups composed of helpers and multiple male and female breeders. Behavioral observations and multilocus DNA fingerprinting have indicated that the social and genetic mating systems of these two species are diverse. Extra‐group paternity appears to be common in both species, necessitating the use of single locus genetic methods to efficiently search for fathers. We therefore characterized 19 microsatellite loci for these two species (12 for magpie‐jays and seven for brown jays) to aid in parentage studies. 相似文献
3.
J. Hinrich G.v.d. Schulenburg Ulrike Englisch J.-Wolfgang Wägele 《Journal of molecular evolution》1999,48(1):2-12
A comparison of ribosomal internal transcribed spacer 1 (ITS1) elements of digenetic trematodes (Platyhelminthes) including
unidentified digeneans isolated from Cyathura carinata (Crustacea: Isopoda) revealed DNA sequence similarities at more than half of the spacer at its 3′ end. Primary sequence similarity
was shown to be associated with secondary structure conservation, which suggested that similarity is due to identity by descent
and not chance. Using an analysis of apomorphies, the sequence data were shown to produce a distinct phylogenetic signal.
This was confirmed by the consistency of results of different tree reconstruction methods such as distance approaches, maximum
parsimony, and maximum likelihood. Morphological evidence additionally supported the phylogenetic tree based on ITS1 data
and the inferred phylogenetic position of the unidentified digeneans of C. carinata met the expectations from known trematode life-cycle patterns. Although ribosomal ITS1 elements are generally believed to
be too variable for phylogenetic analysis above the species or genus level, the overall consistency of the results of this
study strongly suggests that this is not the case in digenetic trematodes. Here, 3′ end ITS1 sequence data seem to provide
a valuable tool for elucidating phylogenetic relationships of a broad range of phylogenetically distinct taxa.
Received: 20 October 1997 / Accepted: 24 March 1998 相似文献
4.
Thomas A. Gorr Barbara K. Mable Traute Kleinschmidt 《Journal of molecular evolution》1998,47(4):471-485
Phylogenetic relationships among reptiles were examined using previously published and newly determined hemoglobin sequences.
Trees reconstructed from these sequences using maximum-parsimony, neighbor-joining, and maximum-likelihood algorithms were
compared with a phylogenetic tree of Amniota, which was assembled on the basis of published morphological data. All analyses differentiated α chains into αA and αD types, which are present in all reptiles except crocodiles, where only αA chains are expressed. The occurrence of the αD chain in squamates (lizards and snakes only in this study) appears to be a general characteristic of these species. Lizards
and snakes also express two types of β chains (βI and βII), while only one type of β chain is present in birds and crocodiles.
Reconstructed hemoglobin trees for both α and β sequences did not yield the monophyletic Archosauria (i.e., crocodilians + birds) and Lepidosauria (i.e., Sphenodon+ squamates) groups defined by the morphology tree. This discrepancy, as well as some other poorly resolved nodes, might be
due to substantial heterogeneity in evolutionary rates among single hemoglobin lineages. Estimation of branch lengths based
on uncorrected amino acid substitutions and on distances corrected for multiple substitutions (PAM distances) revealed that
relative rates for squamate αA and αD chains and crocodilian β chains are at least twice as high as those of the rest of the chains considered. In contrast to
these rate inequalities between reptilian orders, little variation was found within squamates, which allowed determination
of absolute evolutionary rates for this subset of hemoglobins. Rate estimates for hemoglobins of lizards and snakes yielded
1.7 (αA) and 3.3 (β) million years/PAM when calibrated with published divergence time vs. PAM distance correlates for several speciation
events within snakes and for the squamate ↔ sphenodontid split. This suggests that hemoglobin chains of squamate reptiles
evolved ∼3.5 (αA) or ∼1.7 times (β) faster than their mammalian equivalents. These data also were used to obtain a first estimate of some
intrasquamate divergence times.
Received: 15 September 1997 / Accepted: 4 February 1998 相似文献
5.
Development of polymorphic tetranucleotide microsatellites for pinyon jays (Gymnorhinus cyanocephalus) 总被引:1,自引:0,他引:1
Joseph D. Busch Russell Benford Talima Pearson Eldon Palmer Russell P. Balda Paul Keim 《Conservation Genetics》2009,10(3):689-691
The pinyon jay (Gymnorhinus cyanocephalus) is a primary seed disperser of pinyon pines (Pinus edulis and P. monophylla). Both the pinyon jay and the pinyon pines are experiencing significant decline. While the pinyon jay is a species of management
value and conservation concern, little is known about its fecundity, among-flock dispersal, and population differentiation.
We initiated genetic studies in pinyon jays using a hybridization enrichment technique to isolate seven polymorphic microsatellite
repeats (AAAG and GATA) from the pinyon jay genome. A locus from the Mexican jay (Aphelocoma ultramarina) that amplifies robustly in pinyon jays is also reported. These eight loci revealed moderate to high diversity in an Arizona
population of pinyon jays (4–36 alleles and H
O 0.42–0.90). As in other species, tetranucleotide repeats produced easily resolved amplification products. 相似文献
6.
Molecular analyses have been used recently to refine our knowledge of phylogenetic relationships within the ciliated protozoa
(phylum Ciliophora). A current Hennigian phylogeny of the orders in the class Colpodea, based on light and electron microscopic
analyses, makes three important assumptions with regard to apomorphic character states, namely, (1) that the kreyellid silver
line evolved early in colpodean phylogeny, separating bryometopids, such as Bryometopus, from all other colpodeans; (2) that the macro–micronuclear complex is an autapomorphy of the cyrtolophosidids, such as Platyophrya; and (3) that merotelokinetal stomatogenesis is an apomorphic character of colpodids, such as Colpoda, Bresslaua, and Pseudoplatyophrya. These predictions of relationships within the class Colpodea were investigated by determining the complete small subunit
rRNA gene sequences for the colpodid Bresslaua vorax, the grossglockneriid Pseudoplatyophrya nana, and the cyrtolophosidid Platyophrya vorax and a partial sequence for the bryometopid Bryometopus sphagni. These sequences were combined with the previously published complete SSrRNA sequences for the colpodid Colpoda inflata and the bursariomorphid Bursaria truncatella. The affiliations were assessed using both distance matrix and maximum-parsimony analyses. The tree topologies for the class
Colpodea were identical in all analyses, with bootstrap support for bifurcations always exceeding 60%. The results suggest
the following. (1) Since the clade including Bryometopus and its sister taxon, Bursaria, is never basal, the kreyellid silver-line system evolved later in colpodean phylogeny and does not separate bryometopids
from all other colpodeans. (2) Since Platyophrya is always the sister taxon to the other five genera, there is a fundamental phylogenetic significance for its macro–micronuclear
complex. (3) Since the colpodids, Colpoda, Bresslaua, and Pseudoplatyophrya, always group in one clade, merotelokinetal stomatogenesis appears to be a derived character state.
Received: 30 June 1998 / Accepted: 3 December 1998 相似文献
7.
Olivier Verneau François Catzeflis Anthony V. Furano 《Journal of molecular evolution》1997,45(4):424-436
We determined ∼215 bp of DNA sequence from the 3′-untranslated region (UTR) of 240 cloned L1 (LINE-1) elements isolated from
22 species of Rattus sensu lato and Rattus sensu stricto murine rodents. The sequences were sorted into different L1 subfamilies, and oligonucleotides cognate to them
were hybridized to genomic DNA of various taxa. From the distribution of the L1 subfamilies in the various species, we inferred
the partial phylogeny of Rattus sensu lato. The four Maxomys species comprise a well-defined clade separate from a monophyletic cluster that contains the two Leopoldamys and four Niviventer species. The Niviventer/Leopoldamys clade, in turn, shares a node with the clade that contains Berylmys, Sundamys, Bandicota, and Rattus sensu stricto. The evolutionary relationships that we deduced agree with and significantly extend the phylogeny of Rattus sensu lato established by other molecular criteria. Furthermore, the L1 amplification events scored here produced a unique
phylogenetic tree, that is, in no case did a character (a given L1 amplification event) appear on more than one branch. The
lack of homoplasy found in this study supports the robustness of L1 amplification events as phylogenetic markers for the study
of mammalian evolution.
Received: 8 November 1996 / Accepted: 11 April 1997 相似文献
8.
Hong Xue 《Journal of molecular evolution》1998,47(3):323-333
The gene superfamily of ligand-gated ion channel (LGIC) receptors is composed of members of excitatory LGIC receptors (ELGIC)
and inhibitory LGIC receptors (ILGIC), all using amino acids as ligands. The ILGICs, including GABAA, Gly, and GluCl receptors, conduct Cl− when the ligand is bound. To evaluate the phylogenetic relationships among ILGIC members, 90 protein sequences were analyzed
by both maximum-parsimony and distance matrix-based methods. The strength of the resulting phylogenetic trees was evaluated
by means of bootstrap. Four major phylogenetic branches are recognized. Branch I, called BZ, for the majority of the members
are known to be related to benzodiazepine binding, is subdivided into IA, composed of all GABAA receptor α subunits, and IB, composed of the γ and ε subunits, which are shown to be tightly linked. Branch II, named NB
for non–benzodiazepine binding, and consisting of GABAA receptor β, δ, π, and ρ subunits, is further subdivided into IIA, containing β subunits; IIB, containing δ, and π subunits;
and IIC, containing ρ subunits. Branch IIIA, composed of vertebrate Gly receptors, is loosely clustered with Branch IIIB,
composed of invertebrate GluCl receptors, to form Branch III, which is designated NA for being non–GABA responsive. Branch
IV is called UD for being undefined in specificity. The existence of primitive forms of GABAA receptor non-β subunits in invertebrates is first suggested by the present analysis, and the identities of sequences p25123
from Drosophila melanogaster, s34469 from Lymnaea stagnalis, and u14635 and p41849 from C. aenorhabditis elegans are determined to be different from their previously given annotations. The proposed branching classification of ILGICs provides
a phylogenetic map, based on protein sequences, for tracing the evolutionary pathways of ILGIC receptor subunits and determining
the identities of newly discovered subunits on the basis of their protein sequences.
Received: 15 April 1997 / Accepted: 11 March 1998 相似文献
9.
D. Casane S. Boissinot B.H.-J. Chang L.C. Shimmin W.-H. Li 《Journal of molecular evolution》1997,45(3):216-226
We sequenced three argininosuccinate-synthetase-processed pseudogenes (ΨAS-A1, ΨAS-A3, ΨAS-3) and their noncoding flanking
sequences in human, orangutan, baboon, and colobus. Our data showed that these pseudogenes were incorporated into the genome
of the Old World monkeys after the divergence of the Old World and New World monkey lineages. These pseudogene flanking regions
show variable mutation rates and patterns. The variation in the G/C to A/T mutation rate (u) can account for the unequal GC contents at equilibrium: 34.9, 36.9, and 41.7% in the pseudogene ΨAS-A1, ΨAS-A3, and ΨAS-3
flanking regions, respectively. The A/T to G/C mutation rate (v) seems stable and the u/v ratios equal 1.9, 1.7, and 1.4 in the flanking regions of ΨAS-A1, ΨAS-A3, and ΨAS-3, respectively. These ``regional' variations
of the mutation rate affect the evolution of the pseudogenes, too. The ratio u/v being greater than 1.0 in each case, the overall mutation rate in the GC-rich pseudogenes is, as expected, higher than in
their GC-poor flanking regions. Moreover, a ``sequence effect' has been found. In the three cases examined u and v are higher (at least 20%) in the pseudogene than in its flanking region—i.e., the pseudogene appears as mutation ``hot'
spots embedded in ``cold' regions. This observation could be partly linked to the fact that the pseudogene flanking regions
are long-standing unconstrained DNA sequences, whereas the pseudogenes were relieved of selection on their coding functions
only around 30–40 million years ago. We suspect that relatively more mutable sites maintained unchanged during the evolution
of the argininosuccinate gene are able to change in the pseudogenes, such sites being eliminated or rare in the flanking regions
which have been void of strong selective constraints over a much longer period. Our results shed light on (1) the multiplicity
of factors that tune the spontaneous mutation rate and (2) the impact of the genomic position of a sequence on its evolution.
Received: 10 February 1997 / Accepted: 21 April 1997 相似文献
10.
Mitochondrial Genes Collectively Suggest the Paraphyly of Crustacea with Respect to Insecta 总被引:9,自引:0,他引:9
Erik García-Machado Malgorzata Pempera Nicole Dennebouy Mario Oliva-Suarez Jean-Claude Mounolou Monique Monnerot 《Journal of molecular evolution》1999,49(1):142-149
Complete sequences of seven protein coding genes from Penaeus notialis mitochondrial DNA were compared in base composition and codon usage with homologous genes from Artemia franciscana and four insects. The crustacean genes are significantly less A + T-rich than their counterpart in insects and the pattern
of codon usage (ratio of G + C-rich versus A + T-rich codon) is less biased. A phylogenetic analysis using amino acid sequences
of the seven corresponding polypeptides supports a sister-taxon status for mollusks–annelid and arthropods. Furthermore, a
distance matrix-based tree and two most-parsimonious trees both suggest that crustaceans are paraphyletic with respect to
insects. This is also supported by the inclusion of Panulirus argus COII (complete) and COI and COIII (partial) sequence data. From analysis of single and combined genes to infer phylogenies,
it is observed that obtained from single genes are not well supported in most topologies cases and notably differ from that
of the tree based on all seven genes.
Received: 25 August 1998 / Accepted: 8 March 1999 相似文献
11.
Bocchetta M Gribaldo S Sanangelantoni A Cammarano P 《Journal of molecular evolution》2000,50(4):366-380
The phylogenetic placement of the Aquifex and Thermotoga lineages has been inferred from (i) the concatenated ribosomal proteins S10, L3, L4, L23, L2, S19, L22, and S3 encoded in
the S10 operon (833 aa positions); (ii) the joint sequences of the elongation factors Tu(1α) and G(2) coded by the str operon tuf and fus genes (733 aa positions); and (iii) the joint RNA polymerase β- and β′-type subunits encoded in the rpoBC operon (1130 aa positions). Phylogenies of r-protein and EF sequences support with moderate (r-proteins) to high statistical confidence (EFs) the placement of the two hyperthermophiles at the base of the bacterial clade
in agreement with phylogenies of rRNA sequences. In the more robust EF-based phylogenies, the branching of Aquifex and Thermotoga below the successive bacterial lineages is given at bootstrap proportions of 82% (maximum likelihood; ML) and 85% (maximum
parsimony; MP), in contrast to the trees inferred from the separate EF-Tu(1α) and EF-G(2) data sets, which lack both resolution
and statistical robustness. In the EF analysis MP outperforms ML in discriminating (at the 0.05 level) trees having A. pyrophilus and T. maritima as the most basal lineages from competing alternatives that have (i) mesophiles, or the Thermus genus, as the deepest bacterial radiation and (ii) a monophyletic A. pyrophilus–T. maritima cluster situated at the base of the bacterial clade. RNAP-based phylogenies are equivocal with respect to the Aquifex and Thermotoga placements. The two hyperthermophiles fall basal to all other bacterial phyla when potential artifacts contributed by the
compositionally biased and fast-evolving Mycoplasma genitalium and Mycoplasma pneumoniae sequences are eschewed. However, the branching order of the phyla is tenuously supported in ML trees inferred by the exhaustive
search method and is unresolved in ML trees inferred by the quartet puzzling algorithm. A rooting of the RNA polymerase-subunit
tree at the mycoplasma level seen in both the MP trees and the ML trees reconstructed with suboptimal amino acid substitution
models is not supported by the EF-based phylogenies which robustly affiliate mycoplasmas with low-G+C gram-positives and,
most probably, reflects a ``long branch attraction' artifact.
Received: 22 September 1999 / Accepted: 11 January 2000 相似文献
12.
Direct Calculation of a Tree Length Using a Distance Matrix 总被引:8,自引:0,他引:8
Pauplin Y 《Journal of molecular evolution》2000,51(1):41-47
Comparative studies of tree-building methods have shown minimum evolution to be in general an accurate criterion for selecting
a true tree. To improve the use of this criterion, this paper proposes a method for rapidly and directly calculating a length
of a dichotomous tree without having to resort to branch length calculations. This direct calculation (DC) method applies
to the complete final topology, giving equal importance to each branch after a dichotomy. According to this method, the tree
length S
DC
is S
DC
=∑
i
∑
j
(D
ij
/2
Bij
) = (∑
i<j
∑D
ij
2
Bmax−Bij
)/2
Bmax
−1 where D
ij
is the observed distance between taxa i and j,
B
ij
is the number of branches connecting i and j,
Bmax is the greatest B
ij
in the tree, and the powers of two are due to the dichotomy of the tree. This tree length expression may be used as a rapid
method for selecting the shortest tree from a set of hypothetical or subobtimal trees.
Received: 2 March 2000 / Accepted: 24 March 2000 相似文献
13.
Marie Claude Leclerc Véronique Barriel Guillaume Lecointre Bruno de Reviers 《Journal of molecular evolution》1998,46(1):115-120
Sequences from the two ribosomal DNA internal transcribed spacers (ITS1 and ITS2) were compared among five species of Fucus. Based on the present taxon sampling, parsimony analysis showed that Fucus serratus is the sister-group of the remaining Fucus species when Ascophyllum nodosum was used as an outgroup. The topology of the tree was (Fucus serratus (F. lutarius (F. vesiculosus (F. spiralis+F. ceranoides)))). The extremely low variation observed suggests a very recent radiation of the genus which supports the view widely accepted
that the Fucales are among the most evolutionarily advanced of the brown algae. We further note that sequence differences
between Fucus and Ascophyllum were 28%: this does not rule out the utility of ITS sequences within the Fucaceae. The very low number of informative positions
allows to demonstrate empirically that distance matrix methods group on the basis of symplesiomorphies.
Received: 17 February 1997 / Accepted: 17 April 1997 相似文献
14.
Evolution of the Integrin α and β Protein Families 总被引:4,自引:0,他引:4
Hughes AL 《Journal of molecular evolution》2001,52(1):63-72
A phylogenetic analysis of vertebrate and invertebrate α integrins supported the hypothesis that two major families of vertebrate
α integrins originated prior to the divergence of deuterostomes and protostomes. These two families include, respectively,
the αPS1 and αPS2 integrins of Drosophila melanogaster, and each family has duplicated repeatedly in vertebrates but not in Drosophila. In contrast, a third family (including αPS3) has duplicated in Drosophila but is absent from vertebrates. Vertebrate αPS1 and αPS2 family members are found on human chromosomes 2, 12, and 17. Linkage
of these family members may have been conserved since prior to the origin of vertebrates, and the two genes duplicated simultaneously.
A phylogenetic analysis of β integrins did not clearly resolve whether vertebrate β integrin genes duplicated prior to the
origin of vertebrates, although it suggested that at least the gene encoding vertebrate β4 may have done so. In general, the
phylogeny of neither α nor β integrins showed a close correspondence with patterns of α–β heterodimer formation or other functional
characteristics. One major exception to this trend involved αL, αM, αX, and αD, a monophyletic group of immune cell-expressed
α integrins, which share a number of common functional characteristics and have evolved in coordinated fashion with their
β integrin partners.
Received: 22 June 2000 / Accepted: 11 September 2000 相似文献
15.
A mitochondrial DNA (mtDNA) phylogeny of cichlid fish is presented for the most taxonomically inclusive data set compiled
to date (64 taxa). 16S rDNA data establish with confidence relationships among major lineages of cichlids, with a general
pattern congruent with previous morphological studies and less inclusive molecular phylogenies based on nuclear genes. Cichlids
from Madagascar and India are the most basal groups of the family Cichlidae and sister to African–Neotropical cichlids. The
cichlid phylogeny suggests drift-vicariance events, consistent with the fragmentation of Gondwana, to explain current biogeographic
distributions. Important phylogenetic findings include the placement of the controversial genus Heterochromis basal among African cichlids, the South American genus Retroculus as the most basal taxon of the Neotropical cichlid assemblage, and the close relationship of the Neotropical genera Cichla with Astronotus rather than with the crenicichlines. Based on a large number of South American genera, the Neotropical cichlids are defined
as a monophyletic assemblage and shown to harbor significantly higher levels of genetic variation than their African counterparts.
Relative rate tests suggest that Neotropical cichlids have experienced accelerated rates of molecular evolution. But these
high evolutionary rates were significantly higher among geophagine cichlids.
Received: 18 September 1998 / Accepted: 16 December 1998 相似文献
16.
Retroprocessed pseudogenes, calmodulin II (ψ1, ψ2, and ψ3 CALMII), ψα-tubulin, π-glutathione S-transferase (ψπ-GST) from rat, lactic acid dehydrogenase (ψ LDH) from mouse, and heat shock protein 60 chaperonin (ψ HSP60)
from Chinese hamster, were examined for their presence in these species by polymerase chain reaction (PCR). Pseudogenes of
these murine rodents were detected by PCR only in those species in which the genes were originally identified, suggesting
that the selected pseudogene of one species arose too recently to be detected in the genomes of the other rodent species.
The calculated ages of the rodent pseudogenes ranged from 1.7 Myr (ψα-tubulin) to 7.5 Myr (ψ3 CALMII) when employing a homologous functional gene of the taxon as a reference in the relative rate test with the mouse
or rat as the outgroup. Given the high rate of divergence of the genes of rodents relative to other species, selection of
an outgroup with similar mutation rates seems warranted. To justify further the conclusion that the selected pseudogenes were
indeed retroprocessed after these three taxa diverged, the presence of the pseudogenes in the genome of different rat species
was examined. The existence of ψ3 CALMII and ψα-tubulin pseudogenes of Rattus norvegicus among species belonging to Rattus sensu stricto is evidence for the common ancestry of this group.
Received: 23 May 2001 / Accepted: 31 May 2001 相似文献
17.
18.
A revised evolutionary history of hepatitis B virus (HBV) 总被引:8,自引:0,他引:8
Previous studies of the evolutionary history of hepatitis B virus (HBV) have been compromised by intergenotype recombination
and complex patterns of nucleotide substitution, perhaps caused by differential selection pressures. We examined the phylogenetic
distribution of recombination events among human HBV genotypes and found that genotypes A plus D, and genotypes B plus C,
had distinct patterns of recombination suggesting differing epidemiological relationships among them. By analyzing the nonoverlapping
regions of the viral genome we found strong bootstrap support for some intergenotypic groupings, with evidence of a division
between human genotypes A–E from the viruses sampled from apes and human genotype F. However, the earliest events in the divergence
of HBV remain uncertain. These uncertainties could not be explained by differential selection pressures, as the ratio of nonsynonymous-to-synonymous
substitutions (d
N/d
S) did not vary extensively among lineages and there is no strong evidence for positive selection across the whole tree. Finally,
we provide a new estimate of the mean substitution rate in HBV, 4.2 × 10−5, which suggests that divergence of HBV in humans and apes has occurred only in the last 6000 years. 相似文献
19.
We analyzed the phylogenetic relationship between the species of Lordiphosa and other Drosophilidae using alcohol dehydrogenase (Adh) gene sequences. The phylogenetic trees consistently show that the four species Drosophila kurokawai, D. collinella, D. stackelbergi, and D. clarofinis, which include three species groups of Lordiphosa, form a monophyletic clade. This clade is placed as a sister group to the willistoni and saltans groups of Sophophora. On the other hand, three species of Lordiphosa, D. tenuicauda, D. pseudotenuicauda, and D. acutissima, all of which belong to the tenuicauda group, are not shown to be related to the major Lordiphosa lineage. In the phylogenetic trees, these species are included into the clade comprised of Drosophila and Hirtodrosophila, although it remains uncertain whether the tenuicauda group is a monophyletic group or not. These results indicate that Lordiphosa is polyphyletic and that most of the members of the subgenus have a close relationship to the neotropical groups of Sophophora. The above conclusion is compatible with the hypothesis of Okada (Mushi [1963] 37:79–100) and Lastovka and Máca (Acta Ent Bohemoslov [1978] 75:404–420) that Lordiphosa is most closely related to Sophophora; in contrast, our results contradict the hypothesis of Grimaldi (Bull Am Mus Nat Hist [1990] 197:1–139) that Lordiphosa is a sister group to the genus Scaptomyza.
Received: 12 May 1999 / Accepted: 14 April 2000 相似文献
20.
Jon P. Anderson Allen G. Rodrigo Gerald H. Learn Yang Wang Hillard Weinstock Marcia L. Kalish Kenneth E. Robbins Leroy Hood James I. Mullins 《Journal of molecular evolution》2001,53(1):55-62
Phylogenetic analyses frequently rely on models of sequence evolution that detail nucleotide substitution rates, nucleotide
frequencies, and site-to-site rate heterogeneity. These models can influence hypothesis testing and can affect the accuracy
of phylogenetic inferences. Maximum likelihood methods of simultaneously constructing phylogenetic tree topologies and estimating
model parameters are computationally intensive, and are not feasible for sample sizes of 25 or greater using personal computers.
Techniques that initially construct a tree topology and then use this non-maximized topology to estimate ML substitution rates,
however, can quickly arrive at a model of sequence evolution. The accuracy of this two-step estimation technique was tested
using simulated data sets with known model parameters. The results showed that for a star-like topology, as is often seen
in human immunodeficiency virus type 1 (HIV-1) subtype B sequences, a random starting topology could produce nucleotide substitution
rates that were not statistically different than the true rates. Samples were isolated from 100 HIV-1 subtype B infected individuals
from the United States and a 620 nt region of the env gene was sequenced for each sample. The sequence data were used to obtain a substitution model of sequence evolution specific
for HIV-1 subtype B env by estimating nucleotide substitution rates and the site-to-site heterogeneity in 100 individuals from the United States.
The method of estimating the model should provide users of large data sets with a way to quickly compute a model of sequence
evolution, while the nucleotide substitution model we identified should prove useful in the phylogenetic analysis of HIV-1
subtype B env sequences.
Received: 4 October 2000 / Accepted: 1 March 2001 相似文献