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PHYLOGENY OF DIPLOXYLON PINES (SUBGENUS PINUS)
Abstract
The plastid DNA sequences of rbcL, mutK, the trnV intron and the rp120-rps18 spacer were analyzed
among 39 species of subgenus Pinus. A total of 3932 bp were used to assess relationships using MP, NJ
and ML algorithms. Subgenus Pinus splits into two distinct lineages, corresponding to Eurasia and North
America ("New World hard pines"). The Eurasian lineage was differentiated into two clades; the
Mediterranean pines including the Himalayan pine, P roxburghii (subsections Cunurienses, Pineu,
Hulepenses, and Pinuster), and subsection Pinus. Two North American pines, R tropicalis and R resinoscc,
are typical members of subsection Pinus but did not cluster together. Subsection Contortae occupied the
basal position in the "New World hard pines" followed by subsection Ponderosae. The members of
subsection Australes from south of U.S. formed a strongly supported clade sister to the remaining species.
Of remaining "New World hard pines" subsections, Attenuutae was a monophyletic group, and Oocurpae,
Leiophyllue and Australes (FloridaICaribbean species) were poorly resolved. Autrules was paraphyletic in
our phylogeny. The divergence times for each subsection were estimated from the rbcL sequence data.
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We used restriction fragment analysis of chloroplast, nuclear, and mitochondrial DNA to study phylogeny in the genus Pinus. Total genomic DNA of 18 to 19 pine species that spanned 14 of the 15 subsections in the genus was cut with 8 restriction enzymes, blotted, and then probed with up to 17 cloned DNA fragments-which were mostly from the chloroplast genome of Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). A total of 116 shared characters, the majority representing single point mutations, were subjected to Wagner and Dollo parsimony analyses, coupled with bootstrapping and construction of consensus trees. The hard (subgenus Pinus) and soft pines (subgenus Strobus) were distinct. The soft pines in section Parrya, represented by P. longaeva, edulis, monophylla, and gerardiana, were the group closest to the hypothesized root of the genus. They were also more diverse and more closely related to the hard pines than were their descendents in section Strobus, represented by P. koraiensis, albicaulis, griffithii, and lambertiana, all of which were remarkably similar. Except for a strong clade involving P. canariensis and pinea (section Ternatae), the hard pines were weakly differentiated. The high similarity within the most speciose groups of pines (sections Strobus and Pinus) suggests that the bulk of the genus radiated relatively recently. In contrast to a recent classification, P. leiophylla was not associated with section Ternatae; instead, it appears to belong in section Pinus, and showed a high similarity to P. taeda of subsection Australes. Subsection Oocarpae, represented by P. oocarpa and radiata, appears to be a natural group, and is related to subsection Contortae, represented by P. contorta. More extensive restriction fragment studies will yield many new insights into evolution in the genus. Other methods, however, such as DNA sequencing or fine structure analysis of restriction site mutations, are likely to be necessary for rooting pine phylogenies with respect to other coniferous genera, and for estimating divergence times.
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
Accumulating evidence demonstrates that the similarities between the Tertiary and extant floras of Europe and North America have evolved over a long time. The oldest affinities lie in the Late Paleozoic, but the important modern patterns of conifer and angiosperm distribution stem from the later Cretaceous and Tertiary. This floristic exchange took place by both the North Atlantic Land Bridge and the Bering Land Bridge. During the Early Tertiary the North Atlantic Route lay at a substantially lower palcolatitude and afforded both warmer temperatures and more winter light than did the Bering Land Bridge. Post-Eocene climatic cooling increasingly restricted exchange on both routes to temperate taxa. While the Bering Land Bridge remained operational throughout the rest of the Tertiary, geologic evidence suggests the North Atlantic Bridge was physically broken by the Late Eocene, although botanical evidence suggests continued, perhaps sporadic, exchange occurred through to the present, increasingly biased towards cool-tempcrate and ultimately Arctic organisms.
Since Pinus occurs in the Early Cretaceous (ca. 125-130 Ma), it probably had emerged from a Pityostrobus complex by the Late Jurassic (ca. 140-135 Ma). Initial adaptation to seasonal climate and drier sites may account for rapid evolution on several occasions. This presumably was enhanced by symbiotic association with ectotrophic mycorrhizae that gave pines an adaptive advantage in new, spreading, more stressful environments throughout its history. Pinus probably underwent major splitting into early subsections in the Late Cretaceous-Early Tertiary as Laramide tectonism created new environments (dry slopes, rain shadows). In the later Eocene-Oligocene, new opportunities for speciation resulted from increased tectonism, volcanism, and the spread of regional dry climate. New drier sites appeared in the Late Oligocene (28-27 Ma) as erosion increased in response to lowered base level as sea level decreased and as Drakes Passage opened and cold water was shunted northward. Further speciation no doubt occurred as seasonally dry climates spread in response to developing ice sheets (East Antarctic, 13 Ma; West Antarctic, 7-6 Ma; Arctic, 4-3 Ma). Continued volcanism, tectonism, and markedly fluctuating climate at the close of the Cenozoic fostered further speciation, especially in Mexico where pines show much intergradation owing to rampant hybridization in the recent past. Species of three subsections (Cembrae, Strobi, Sylvestres) in North America are represented by taxa in Eurasia. They reflect the early spread of ancestral taxa into both land areas via connections across the mid-to-north Atlantic and Beringian areas. Neogene records in Europe of taxa allied to east American pines (Australes) may be valid but need reevaluation. The fossil record suggests that six of the eight subsections indigenous to North America (Balfourianae, Cembroides, Leiophyllae, Oocarpae, Ponderosae, Sabinianae) probably originated over the Cordilleran region that extends southward into Mexico. Subsect. Australes may be largely southeastern and the Contortae evidently spread northward (P. contorta, P. banksiana) and into mountains as colder environments appeared there. Movement along the San Andreas rift system probably transported taxa northward from western Mexico, as indicated by species of Oocarpae, Leiophyllae, and Strobi in Tertiary rocks of coastal California. As more extreme climates spread in the late Cenozoic, the richer Tertiary forests and woodlands lost taxa, and the survivors retreated to moister areas. Pines now increased numerically as competition was reduced and more space appeared in the impoverished, surviving vegetation zones. In addition, spreading new regional environments, notably drier lowlands (for pinons), drier upland slopes (for P. ponderosa, P. scopulorum, P. jeffreyi, P. flexilis), colder, wetter basins (for P. banksiana, P. contorta), and cold uplands (for P. albicaulis, P. aristata, P. contorta, P. monticola), now became available as more continental climates spread. Pines in these more extreme environments, where they are also associated with ectotrophic mycorrhizae, may form regionally extensive, pure stands. These are not recorded in presently-known Tertiary floras in which pines were members of rich, mixed conifer, conifer hardwood, and sclerophyllous woodland vegetation. During the past few centuries, some pines greatly increased in number as man upset ecosystems by fire, logging, and clearing.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
We used restriction fragment analysis of chloroplast, nuclear, and mitochondrial DNA to study phylogeny in the genus Pinus. Total genomic DNA of 18 to 19 pine species that spanned 14 of the 15 subsections in the genus was cut with 8 restriction enzymes, blotted, and then probed with up to 17 cloned DNA fragments-which were mostly from the chloroplast genome of Douglasfir (Pseudotsuga menziesii [Mirb.] Franco). A total of 116 shared characters, the majority representing single point mutations, were subjected to Wagner and Dollo parsimony analyses, coupled with bootstrapping and construction of consensus trees. The hard (subgenus Pinus) and soft pines (subgenus Strobus) were distinct. The soft pines in section Parrya, represented by P. longaeva, edulis, monophylla, and gerardiana, were the group closest to the hypothesized root of the genus. They were also more diverse and more closely related to the hard pines than were their descendents in section Strobus, represented by P koraiensis, albicaulis, griffithii, and lambertiana, all of which were remarkably similar. Except for a strong clade involving P. canariensis and pinea (section Ternatae), the hard pines were weakly differentiated. The high similarity within the most speciose groups of pines (sections Strobus and Pinus) suggests that the bulk of the genus radiated relatively recently. In contrast to a recent classification, P. leiophylla was not associated with section Ternatae; instead, it appears to belong in section Pinus, and showed a high similarity to P taeda of subsection Australes. Subsection Oocarpae, represented by P. oocarpa and radiata, appears to be a natural group, and is related to subsection Contortae, represented by P contorta. More extensive restriction fragment studies will yield many new insights into evolution in the genus. Other methods, however, such as DNA sequencing or fine structure analysis of restriction site mutations, are likely to be necessary for rooting pine phylogenies with respect to other coniferous genera, and for estimating divergence times.