Deriving Phylogenetic Trees from Allele Frequencies: A Comparison of Nine Genetic Distances

Rogers, J. S.

doi:10.2307/2413383

Cited by 35 publications

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“…Alleles were given alphabetic designations in order of decreasing mobility. Rogers' (1972) and Nei's (1978) distance values were calculated for analyses of within-species variation and for comparative purposes with earlier studies.…”

Section: Methodsmentioning

confidence: 99%

“…Opting for a phylogenetic method of analysis would result in loss of information because only one character state can be assigned to a particular taxon at a given locus. Consequently, distance-Wagner trees (Farris, 1972) based on Cavalli-Sforza and Edward's (1967) chord distance (Nei et al, 1983;J. S. Rogers, 1986) were constructed by use of the BIOSYS-1 computer program (Swofford and Selander, 1981).…”

Section: Methodsmentioning

confidence: 99%

“…1). The Rogers' (1972) distance value separating samples 24 and 25 is 0.114, and is attributable to a single fixed allelic difference and to frequency differences at four loci. Sample 27, initially identified as H. australis based on its geographic location (eastern Panama), is genically and morphologically (D. S. ) most similar to the two H. anomalus samples.…”

Section: Intraspecific Variationmentioning

confidence: 96%

“…Sample 27, initially identified as H. australis based on its geographic location (eastern Panama), is genically and morphologically (D. S. ) most similar to the two H. anomalus samples. Rogers' (1972) distance values between sample 27 and samples 24 and 25 are 0.283 and 0.262, respectively. Fixed differences at seven loci account for most of the differentiation.…”

Section: Intraspecific Variationmentioning

confidence: 98%

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Genic Evolution, Historical Biogeography, and Systematic Relationships Among Spiny Pocket Mice (Subfamily Heteromyinae)

Rogers

1990

Journal of Mammalogy

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ABSTRAGr.-Protein variation at 30 presumptive gene loci was examined among 36 populations comprising all species of spiny pocket mice (subfamily Heteromyinae). The bulk of betweensample genic variation involved fixed allelic differences. A distance-Wagner tree divided the heteromyines into two groups, one formed by Heteromys gaumeri and the other composed of all remaining taxa. Within this latter group, species of HeteTomys comprising the anomalus species group were genically most similar to members of the genus Liomys. A consensus distance-Wagner tree constructed by use of the jackknifing approach yielded eight unresolved lineages of heteromyines. Genic data support the monophyly of heteromyines relative to other heteromyid rodents, but do not support monophyly of Heteromys and Liomys. Allozyme data were mostly concordant with karyotypic data, but failed to support recent taxonomies based on morphological characters regarding interspecific relationships among species of HeteTomys. Genic and karyotypic data indicate that H. desmaTestianus is divisible into two moieties in southern Mexico, H. goldmani is not differentiated from geographically adjacent populations of H. desmaTestianus, and H. OTesteTus is not closely allied with H. nelsoni. Based on allozyme data, H. anomalus and H. austTalis are not closely related. Affinities among species of Liomys derived from allozyme data were in agreement with those based on morphological and chromosomal information, but indicate that L. pictus, as currently constituted, is paraphyletic. The amount of genic divergence within Heteromys from South America most likely precludes the gwerally accepted view of a recent invasion of South America by these mice.Spiny pocket mice of the heteromyid subfamily Heteromyinae (genera HeteTomys and Liomys-Honacki et aI., 1982) are a group in which morphological parallelism is widespread (Wood, 1935). Fossil remains are known from Pliocene, Pleistocene, and Holocene depositions but are indistinguishable from extant forms (Alvarez, 1982;Wood, 1935). Morphological variation within the subfamily is fairly well documented, and the view that heteromyines form a monophyletic lineage has never been contested. Among the morphological characters distinguishing Heteromys and Liomys from other heteromyids are several shared derived characters of the glans penis (Hafner and Hafner, 1983), exomorphology (Wood, 1935), and hair microstructure (Homan and Genoways, 1978). Genoways (1973) reduced the number of species in the genus Liomys from 11 to five, dividing these into three groups as follows: L. irroratus, L. pictus and L. spectabilis, and L. salvini and L. adspersus. In his revision, Goldman (1911) recognized 13 species of Heteromys, dividing them among two subgenera (Heteromys and Xylomys). He further divided the nominate subgenus into two species groups, anomalus and desmarestianus. Rogers and Schmidly (1982) evaluated the systematic relationships of H. desmarestianus, H. lepturus, H. longicaudatus, H. goldmani, and H. temporalis by examining variatio...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Intraspecific Variationmentioning

confidence: 96%

Section: Intraspecific Variationmentioning

confidence: 98%

See 2 more Smart Citations

Genic Evolution, Historical Biogeography, and Systematic Relationships Among Spiny Pocket Mice (Subfamily Heteromyinae)

Rogers

1990

Journal of Mammalogy

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“…In the phenetic approach, a matrix of Nei's unbiased (DN; Nei, 1978) and Rogers' genetic distances (DR; Rogers, 1972) was computed, but because the former distance is not a metric (Rogers, 1986) only the latter will be used in subsequent analyses. The genetic relationships of the taxa were reconstructed with the distance-Wagner procedure (Farris, 1972).…”

Section: Plylogenetic Reconstmctionmentioning

confidence: 99%

Phylogenetic evolution and biogeography of Southeast Asian shrews (genus Crocidura: Soricidae)

Rüedi¹

1996

Biological Journal of the Linnean Society

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Genetic variation of 20 species of shrews from the Malay peninsula, Sumatra, Java, Borneo, the Philippines and Sulawesi was assessed by allozyme electrophoresiis at 32 loci. According to Mantel's tests, the genetic differentiation of these species of shrews is not a function of the geographic distance separating them (r = 0.09, NS), but is correlated to the water depth surrounding the islands where they live (r = 0.49, P < 0.01). The results are just the reverse if the correlations are computed for the Sunda Shelf taxa only. In this case, the sampled populations show an isolation-by-distance relationship (r = 0.32; P < 0.01), while no significant correlation with water depth was detected (r = 0.20; P = 0.07).Qualitative predictions based on eustatic sea level variation and water depth were formulated as a model of historic connections between the islands. This palaeogeographic model was tested through Brooks Parsimony Analysis. The assumption of a simple vicariant evolution of the shrews was rejected, but several concordant patterns indicate that the phylogeny of these mammals was indeed shaped by these events. Homoplasies demonstrated that the SE Asian species of Crocidura include composite zoogeographic histories. Sulawesi, for example, supports at least six species, five of which are closely related, while the last one, C. n w e s , is more closely related to a Bornean taxon. This pattern was interpreted as the result of a fmt wave of colonizers which subsequently radiated, followed by a more recent, second colonization event from Borneo. The overall small genetic distance found within the assemblage of the five old endemics (DN = 0.151 f 0.041) suggests that the radiation was not accompanied by extensive differentiation, although from a karyological point of view, they exhibit unusual variations when compared to other Indomalayan Crdura. By contrast, the four species found on Sumatra are more differentiated (DN = 0.221 f 0.063) and never form sister-group relationships in any phylogenetic reconstruction; each one is more closely related to different taxa living outside Sumatra. This suggests that they are probably remnants of an important centre of dispersal for the entire Malay Archipelago. The standard genetic distance averaged among all Southeast Asian species (DN = 0.235 f 0.094) is about half that measured within Palearctic or African taxa. Such an overall lower mean level of genetic variability is consistent with the hypothesis of a relatively recent colonization of the Malay Archipelago by shrews of the genus Crocidura.

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Platyrrhine systematics: A simultaneous analysis of molecular and morphological data

Horovitz

Zardoya

Meyer

1998

Am. J. Phys. Anthropol.

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Platyrrhine phylogeny has been investigated repeatedly with morphological characters and DNA nuclear gene sequences, with partially inconsistent results. Given the finding in the past decade that the mitochondrial genome is a potentially valuable source of phylogenetic information, we gathered DNA sequence data of a fragment of the 16S and the entire 12S mitochondrial genes. The objectives were to generate a cladistic phylogeny based on these data and to combine them in a simultaneous analysis with morphological characters and preexisting nuclear DNA sequences. Mitochondrial data analyzed on its own yielded a cladogram that was different from those generated with other data sets. The simultaneous analysis of mitochondrial, nuclear, and morphological data yielded a tree most congruent with that generated with nuclear data and to a lesser degree with the morphological one. It depicted a basal dichotomy that led to two major clades: one of them comprised [Atelinae (Callicebus ϩ Pitheciini)] and the other major clade comprised [Aotus ((Cebus, Saimiri) (Callitrichinae))]. The weakest point of the phylogeny was the position of Aotus as basal within their clade as opposed to more closely linked with either the callitrichines or Cebus-Saimiri. Relationships within callitrichines and atelines were unstable as well. The simultaneous phylogenetic analysis of all data sets revealed congruent signal in all of them that was partially obscured in the separate analyses. Am J Phys

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Deriving Phylogenetic Trees from Allele Frequencies: A Comparison of Nine Genetic Distances

Cited by 35 publications

References 0 publications

Genic Evolution, Historical Biogeography, and Systematic Relationships Among Spiny Pocket Mice (Subfamily Heteromyinae)

Genic Evolution, Historical Biogeography, and Systematic Relationships Among Spiny Pocket Mice (Subfamily Heteromyinae)

Phylogenetic evolution and biogeography of Southeast Asian shrews (genus Crocidura: Soricidae)

Platyrrhine systematics: A simultaneous analysis of molecular and morphological data

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