k-casein gene phylogeny of higher ruminants (pecora, artiodactyla)

MOLECULAR PHYLOGENETICS AND EVOLUTION

Vol. 6, No. 2, October, pp. 295–311, 1996ARTICLE NO. 0078

K-Casein Gene Phylogeny of Higher Ruminants(Pecora, Artiodactyla)1

MATTHEW A. CRONIN,2 RICHARD STUART, BARBARA J. PIERSON, AND JOHN C. PATTON

LGL Ecological Genetics, Inc., 1410 Cavitt Street, Bryan, Texas 77801

Received October 11, 1995; revised March 25, 1996

Scott, 1987; Irwin et al., 1993). However, there is notTo assess phylogenetic relationships among the a consensus on the systematic relationships of the pec-

higher ruminants (infraorder Pecora, order Artiodac- oran families or lower taxa. Morphological studies havetyla), we analyzed K-casein DNA sequences, includ- resulted in alternative phylogenetic groupings of fiveing 434 nucleotides of the fourth exon. The higher families: Antilocapridae (pronghorns), Bovidae (cattle,ruminant families Bovidae, Cervidae, Giraffidae, and sheep, antelope), Cervidae (deer), Moschidae (muskAntilocapridae each have monophyletic K-casein se- deer), and Giraffidae (giraffes and okapis). In the differ-quences. Maximum parsimony and distance analyses ent schemes, moschids, antilocaprids, and giraffids oc-identify Giraffidae as a sister group to either Cervidae cur in clades with either cervids or bovids or in an unre-or a Bovidae-Cervidae clade and Antilocapridae as a solved polychotomy. Tragulidae (chevrotains or mousesister group to a Bovidae–Cervidae–Giraffidae clade. deer) are ruminants, but are distinguished from theAt a higher level these four families occur as a mono- pecorans by several characters. A recent review of pec-phyletic clade relative to Tragulidae and Suidae.

oran systematics is provided by Janis and Scott (1987).Within Cervidae, the subfamily Odocoileinae is mono-Within the Cervidae, the common classification in-phyletic and Cervinae and Muntiacinae occur as inde-

cludes two major subfamilies which differ in morphol-pendent lineages within a separate clade. Withinogy and behavior (Geist, 1982; Groves and Grubb, 1987;Bovidae, the subfamilies Bovinae and CaprinaeJanis, 1988). The Cervinae occur in Eurasia (exceptare monophyletic. Genera within Cervinae (Cervus,North American elk, Cervus elaphus). The OdocoileinaeElaphurus) and Bovinae (Bison, Bos) are paraphyletic.includes North American Odocoileus (white-tailedThere is intraspecific allelic variation in Cervus ela-deer, black-tailed deer, mule deer), Eurasian Capreolusphus, Odocoileus hemionus, and Bison bison. The rate(roe deer), and several South American genera, includ-of K-casein fourth exon DNA sequence evolution is es-

timated to be about 0.004 nucleotide substitutions per ing Mazama (brockets). The holarctic moose (Alcesmillion years. The K-casein phylogeny is discussed rel- alces) and caribou (Rangifer tarandus) lineages areative to other molecular and morphological data. considered either tribes within the Odocoileinae 1996 Academic Press, Inc. (Groves and Grubb, 1987) or separate subfamilies

(Gustafson, 1985; Bubenik, 1990). Additional subfami-lies include Hydropotinae (water deer), Moschinae(musk deer, also given family status as mentioned

INTRODUCTION above), and Muntiacinae (muntjacs) (Simpson, 1945;Nowak and Paradiso, 1983). Muntjacs have also been

The higher ruminants (Pecora, Artiodactyla) have given family status (Bubenik, 1990) or tribe statusbeen the subject of considerable evolutionary study be- (Groves and Grubb, 1987) within the Cervinae. Withincause of their enormous physiological and ecological Bovidae, there are at least five subfamilies and asflexibility, good fossil record, and rapid radiation which many as 14 tribes (Simpson, 1945; Meester and Setzer,includes about 120 extant and 300 extinct species (e.g., 1971; Vaughan, 1978; Nowak and Paradiso, 1983; Al-Gould, 1974; Honacki et al., 1982; Savage and Russell, lard et al., 1992). Two widely recognized subfamilies1983; Guthrie, 1984; Geist, 1987; Vrba, 1987; Janis and are Bovinae (e.g., cattle, bison, buffalos) and Caprinae

(e.g., sheep, goats). There are two extant genera of1 Sequence data from this article have been deposited with the Giraffidae (Okapia, Giraffa) and one of Antilocapridae

GenBank Data Libraries under Accession Nos. U37279, U37360– (Antilocapra).U37363, and U37502–U37516. Genetic data have been used in systematic studies2 To whom correspondence should be addressed at LGL Alaska Re-

of these taxa including allozymes (Baccus et al., 1983;search Associates, Inc., 4175 Tudor Centre Drive, Suite 202, Anchor-age, AK 99508. Fax: (907) 562-7223. E-mail: [email protected]. Georgiadis et al., 1990; Emerson and Tate, 1993), pro-

2951055-7903/96 $18.00Copyright 1996 by Academic Press, Inc.All rights of reproduction in any form reserved.

296 CRONIN ET AL.

tein sequences (Mross and Doolittle, 1967; Doolittle et independent origin (Stewart et al., 1984; Alexander etal., 1988). All four casein genes are linked on bovineal., 1967; Beintema et al., 1986, 1988; Graur and Hig-

gins, 1994), mitochondrial DNA (mtDNA; Miyamoto et chromosome 6 (Grosclaude et al., 1973; Fries et al.,1993; Bishop et al., 1994).al., 1990; Cronin, 1991, 1994; Irwin et al., 1991; Kraus

and Miyamoto, 1991; Allard et al., 1992; Gatesy et al., Κ-Casein alleles with varying effects on milk qualityhave been detected in dairy cattle and are potentially1992; Kraus et al., 1992), repetitive DNA (Lima-de-

Faria et al., 1984), nuclear ribosomal DNA (Wall et useful in artificial selection programs (Schaar et al.,1985; Pinder et al., 1991). Among artiodactyls, mostal., 1992), nuclear lysozyme genes (Irwin et al., 1992,

1993), single copy genomic DNA–DNA hybridization Κ-casein research has focused on bovids and caprids,although Cronin et al. (1995) describe intraspecific(Tronick et al., 1977; Cronin, 1989), immunological dis-

tances (Wilson et al., 1974), and chromosomes (Todd, variation in Κ-casein in a cervid, Rangifer tarandus. In-terspecific comparisons have been limited, although1975; Gallagher et al., 1994). These studies have gener-

ally suggested the artiodactyl families and subfamilies Cronin and Cockett (1993) and Sipko et al. (1994) iden-tified allelic variation in Κ-casein in cattle and bisonare monophyletic, but phylogenetic relationships are

still not definitive. For example, Baccus et al. (1983) (Bison spp.). We report phylogenetic relationships of Κ-casein DNA sequences among several artiodactyl taxa.noted that ‘‘the Cervidae is a group of heterogeneously

related species,’’ and that the bovids, cervids, and an- We specifically compare sequences for a portion of thefourth exon (Alexander et al., 1988) among families andtilocaprids are more closely related than expected for

members of different families. Phylogenetic analyses of lower taxa.mtDNA have shown paraphyletic relationships amongthese three families or an unresolved polychotomy of MATERIALS AND METHODSbovids, cervids, giraffids, and antilocaprids (Irwin etal., 1991; Kraus and Miyamoto, 1991; Gatesy et al., Tissue or blood samples were obtained from 20

taxa in Bovidae, Cervidae, Giraffidae, and Antilocap-1992). In addition, single-copy genomic DNA–DNA hy-bridization experiments did not clearly differentiate bo- ridae (Table 1). DNA was amplified with the poly-

merase chain reaction (PCR; Mullis and Faloona,vids, cervids, and antilocaprids (Tronick et al., 1977;Cronin, 1989). At the subfamily level, mtDNA analyses 1987) using the primers of Pinder et al. (1991): 10592

primer (5′-GTGCTGAG(T/C)AGGTATCCTAG-3′);generally support the monophyly of Odocoileinae andCervinae, although several genera within these sub- 11466 primer (5′-GTAGAGTGCAACAACACTGG-3′).

The primer number indicates the nucleotide position offamilies are paraphyletic (Miyamoto et al., 1990; Cro-nin, 1991). the primer in the bovine Κ-casein sequence (Alexander

et al., 1988). PCR reactions (50 µl) contained 5–50 ngAlthough systematic studies of artiodactyl DNA arerelatively limited, analyses of gene organization and DNA in 10 mM Tris–Cl, pH 8.3, 50 mM KCl, 1.5 mM

MgCl2, 0.2 mM of each dNTP, 1 µM of each of the twofunction are extensive in the animal science literature(e.g., Fries et al., 1993; Bishop et al., 1994; Rohrer et primers, and 1.25 units of Amplitaq DNA polymerase

(Perkin–Elmer, Norwalk, CT). Reactions were heatedal., 1994). We have used methods and data developedfor domestic artiodactyls (cow, sheep, goat, pig) to con- to 95°C for 5 min followed by 32 cycles of amplification.

Each cycle consisted of 45 s at 95°C, 30 s at 50°C, andduct a phylogenetic analysis of a milk protein gene, Κ-casein (Cronin and Cockett, 1993; Cronin et al., 1995; 2.5 min at 70°C. DNA sequences were obtained from

PCR products by direct sequencing (Carr and Marshall,J. E. Gatesy, unpublished manuscript). Κ-Casein ex-pression in mammary gland tissue is controlled by hor- 1991). For sequencing, we used the 10592 primer

and one reported by Schlieben et al. (1991): 11036mones, particularly prolactin (Nakhasi et al., 1984). Inmilk of the domestic cow, calcium phosphate, Κ-casein, primer (5′-TTTGATGTCTCCTTAGAGT-3′). Both DNA

strands were sequenced for all taxa except for Ovisand three calcium-sensitive caseins (α-casein 1, α-casein 2, and β-casein) form aggregates, called milk mi- dalli, Oreamnos americanus, and Bison bison, which

were sequenced using only the 10592 primer. Se-celles, which increase the solubility of the calcium phos-phate (Thompson et al., 1985; Philippe and Douzery, quences for 7 other taxa including Tragulus, Saiga,

Sus, Cervus nippon, Bos, Capra, and Ovis, were ob-1994). Digestion of Κ-casein in the stomach leads toclotting of the milk, which is important for increasing tained from the literature or GenBank (Table 1) giving

a total of 27 taxa.the time of assimilation of nutrients (Mercier et al.,1976). Κ-Casein is thought to have evolved from dupli- Sequences were aligned (Swofford and Olsen, 1990)

with the SeqEd v. 1.0.3 computer program (ABI, Fostercation of a fibrinogen gene, which has a primary clot-ting function in blood (Jolles et al., 1978; Brignon et al., City, CA). Sequences were analyzed for nucleotide com-

position, transition/transversion ratio, and synony-1985; Crabtree et al., 1985; Thompson et al., 1985; Alex-ander et al., 1988). The α- and β-caseins are thought to mous and nonsynonymous substitutions with the

MEGA computer program (Kumar et al., 1993). Phylo-share a common ancestral gene, while Κ-casein has an

Κ-CASEIN PHYLOGENY OF RUMINANTS 297

TABLE 1

Artiodactyl Taxa for Which K-Casein Sequences Were Analyzed

Family Subfamily Species Common name Source of tissue or sequence

Cervidae Odocoileinae Odocoileus virginianus White-tailed deer J. Wickliffe, Brooks Co. TexasO. hemionus hemionus Mule deer Gallatin Co. MontanaO. h. sitkensis Black-tailed deer M. Kirchoff, Revillagigido Is., AlaskaMazama americana Red brocket D. Wharton, Wildlife Conservation SocietyRangifer tarandus Caribou S. Mahoney, Newfoundland, CanadaAlces alces Moose AlaskaCapreolus capreolus Roe deer A. Lima-de-Faria, Univ. Lund, Sweden

Cervinae Cervus elaphus manitobensis Elk R. McClymont and W. Wishart, AlbertaC. e. elaphus Red deer P. Dratch, New ZealandC. nippon Sika deer K. Chikuni, T. Tabata, M. Sato, M. Monma,

GenBank Accession No. D14379C. unicolor Sambar D. Wharton, Wildlife Conservation SocietyC. duvauceli Barashinga D. Wharton, Wildlife Conservation SocietyElaphurus davidianus Pere Davids deer D. Wharton, Wildlife Conservation Society

Muntiacinae Muntiacus reevesi Reeves muntjac O. Ryder, San Diego ZooBovidae Bovinae Bos taurus Domestic cattle Alexander et al. (1988)

Bison bison bison Plains bison J. Bates, D. Jones, Henry Mts., UtahB. b. athabascae Wood bison C. Gates, Northwest Territories, Canada

Caprinae Ovis airies Domestic sheep Furet et al. (1990)O. dalli Dall sheep R. Kahlenbeck, northwest of Tok, AlaskaCapra hircus Domestic goat Coll et al. (1993)Oreamnos americanus Mountain goat Gallatin Co. MontanaOvibos moschatus Musk ox L. Teal, Musk Ox Farm, Palmer, AlaskaSaiga tatarica Saiga K. Chikuni, T. Tabata, M. Sato, M. Monma,

GenBank Accession No. D32188Giraffidae Giraffa camelopardalis Reticulated giraffe B. Read, St. Louis ZooAntilocapridae Antilocapra americana Pronghorn J. Bickham, Brewster Co. TexasTragulidae Tragulus javanicus Mouse deer K. Chukini, T. Tabata, M. Sato, M. Monma,

GenBank Accession No. D14381Suidae Sus scrofa Domestic pig Levine et al. (1992)

genetic analyses were done with maximum parsimony ses, a nonruminant, Sus (domestic pig), was used asan outgroup and insertions/deletions were consideredand distance methods. Parsimony analyses were done

with the branch and bound method (Hendy and Penny, single characters.1982) with both accelerated and delayed character-state optimization using the PAUP version 3.1 com- RESULTSputer program (Swofford, 1993). The branch and boundmethod allows identification of optimal trees without We obtained sequence for 434 nucleotide positions,

including insertions and deletions (Fig. 1). This encom-exhaustive searching. When assigning character-statesat internal nodes, the accelerated optimization option passed the 372 nucleotides within the fourth exon of

the Κ-casein gene between bovine sequence positionprefers single origin and reversal of characters anddelayed optimization prefers parallel origins of the 10642 and the stop codon at position 11014 (Alexander

et al., 1988). Insertions in nonbovine taxa resulted insame character-state. We also conducted a bootstrap(Felsenstein, 1985) analysis (500 replicates) using the the additional 62 nucleotides relative to the bovine se-

quence. Nucleotide composition included relativelyheuristic search option of PAUP. Jukes-Cantor (1969)genetic distances were calculated with the PHYLIP higher proportions of A and C than T and G: A, mean

5 31.1% (range among taxa 27.9–32.2%); C, mean 5(Felsenstein, 1993) and MEGA computer programs.The pairwise-deletion option was used, in which a dis- 29.3% (range 27.4–32.8); T, mean 5 23.1% (range

20.1–24.4%); and G, mean 5 16.9% (range 15.4–tance is calculated for each pair of sequences, ignoringonly gaps (resulting from insertions/deletions) involved 19.2%). Among all pairwise comparisons of taxa, the

transition/transversion ratio was 1.659. The propor-in a specific pairwise comparison. The distances wereused to construct dendrograms with the FITCH option tion of synonymous substitutions per synonymous site

was 0.0903 (SE 5 0.0152), and the proportion of non-of PHYLIP (Fitch and Margoliash, 1967) and theNeighbor Joining (NJ) bootstrap (500 replicates) synonymous substitutions per nonsynonymous site

was 0.0804 (SE 5 0.0084).method of MEGA (Saitou and Nei, 1987). In all analy-

298 CRONIN ET AL.

FIG. 1. Aligned sequences for the fourth exon of artiodactyl Κ-casein. Dots indicate identity with the Odocoileus virginianus sequencein the first row. Dashes indicate gaps at insertion/deletion sites. The first and last nucleotides correspond to positions 10642 and 11014(end of the fourth exon) of the Bos taurus sequence (Alexander et al., 1988).

There are five insertions/deletions in various taxa: Jukes-Cantor distances were calculated for all pair-wise comparisons of taxa, and the ranges, means, and24 nucleotides between positions 104 and 127, present

in all taxa but Sus; 6 nucleotides between positions 255 standard deviations for several taxa are shown in Table2. Although the Jukes-Cantor method considers transi-and 260, which occurred only in Ovis, Capra, Ovibos,

and Oreamos; 36 nucleotides between positions 294 and tions and transversions equally likely, Kumar et al.(1993) recommend it in cases like ours, when the329, which occurred only in Saiga; 18 nucleotides be-

tween positions 338 and 355, present in only Sus; and transition/transversion ratio is ,2.0 and distances are,0.3. Other methods, including that of Kimura (1980)3 nucleotides between positions 378 and 380, present

in only Sus (Fig. 1). which considers the transition/transversion ratio in


FIG. 1—Continued

calculating distances and the proportion of substitu- level, the distances between Muntiacinae and eitherOdocoileinae or Cervinae, and between Bovinae andtions (p; Kumar et al., 1993), gave values similar to

the Jukes-Cantor distances for our sequences (data Caprinae, are particularly high, and similar to inter-family distances.not shown). As shown in Table 2, there is generally

greater distance between higher-level taxa, although The branch and bound parsimony analysis resultedin two maximum parsimony (MP) trees (length 268there is some overlap of values at different taxonomic

levels: within subfamilies 0.0054–0.0589; between steps, consistency index 0.795), which are shown alongwith a strict consensus tree in Fig. 2. The tree topology,subfamilies 0.0387–0.1164; between pecoran families

0.0589–0.1618; between Tragulidae and pecorans total number of steps, and consistency indices for theMP trees were the same with either delayed or acceler-0.1165–0.2031; and between ruminants (pecorans and

Tragulidae) and pig (0.2155–0.2881). At the subfamily ated optimization of character-states. However, the

300 CRONIN ET AL.

FIG. 1—Continued

numbers of characters defining some branches varied gies, we also derived MP trees one step longer than theMP trees in Fig. 2. There were 33 trees 269 steps longdepending on optimization method. The numbers of

characters between nodes, or between nodes and taxa, (consistency index 5 0.795), which we discuss below.The FITCH analysis of the Jukes-Cantor distances ex-are shown on the MP trees. When characters differed

between the delayed and accelerated optimizations, the amined 6791 trees (sum of squares 5 2.04, average %SD 5 5.39) and resulted in the tree shown in Fig. 3.numbers for delayed optimization are shown in paren-

theses on the trees. The branch and bound consensus The NJ analysis resulted in the other tree in Fig. 3,upon which bootstrap values (which range from 57 totree had the same topology as the heuristic bootstrap

consensus tree, and we have put the bootstrap values 100%) are shown.In all trees, including the MP trees 268–269 steps(which range from 59 to 100%) on the nodes of the con-

sensus tree (Fig. 2). To assess alternative tree topolo- long and the FITCH and NJ trees, Antilocapra was the


FIG. 1—Continued

sister group of the large clade containing bovids, cer- the placement of Giraffa. In the MP1 and NJ trees,Giraffa was identified as the sister group of a majorvids, and Giraffa. The monophyly of a bovid–cervid–

giraffid clade is better supported with accelerated clade containing Bovidae and Cervidae, although theNJ bootstrap value was relatively low (70%). In theoptimization (five characters on MP trees) than with

delayed optimization (three or four characters on MP MP2 and FITCH trees, Giraffa was the sister group ofCervidae (Figs. 2 and 3). However, the branch linkingtrees). In the NJ tree, Tragulus was the sister group of

all the other ruminant taxa, and in the MP and FITCH Giraffidae with Cervidae in the MP trees (nodes E–F) isdefined by only two characters, and the branch linkingtrees the relationship of Tragulus and Sus with the

Pecoran was unresolved (Figs. 2 and 3). Bovidae with Cervidae (nodes C–D) is defined by onlyone or three characters, depending on optimizationThe primary topological difference between the two

MP trees, and between the FITCH and NJ trees, was method. There is also a relatively low bootstrap value

302 CRONIN ET AL.

FIG. 1—Continued

(63%) for the bovid–cervid clade in the NJ tree (Fig. 3). the family-level nodes of MP1 and MP2 are shown.Each family is defined by several (4–9) characters atWhen considering the 35 MP trees 268 or 269 steps

long, Giraffa was the sister group of a bovid–cervid each node. There is strong support for cervid mono-phyly from the bootstrap values (96–97%, Figs. 2 andclade in 18 trees, and Giraffa was the sister group of

the cervids in 17 trees. As shown by the trichotomy, 3), and 6–8 characters defining the family. There isless, but substantial, support for bovid monophyly withand the relatively low bootstrap value (64%) in the MP

consensus tree, the relative relatedness of Giraffidae, bootstrap values of 71–79%, and 4–7 characters defin-ing the family. In the MP1 tree, Cervidae is defined byBovidae, and Cervidae Κ-casein sequences must be con-

sidered unresolved with these data. 2 more characters, and Bovidae is defined by 2 fewercharacters, with delayed optimization than with accel-The ruminant family-level relationships are further

characterized in Table 3, in which the numbers of char- erated optimization.The subfamilies, Cervinae, Muntiacinae, and Odo-acters, nucleotide changes, and consistency indices for


FIG. 1—Continued

coileinae, occurred as monophyletic groups within the 2 characters and moderate bootstrap values (63–81%).Within Bovidae, Caprinae and Bovinae occurred as mo-Cervidae in all trees. The Muntiacinae was quite dis-

tinct, was defined by 24–25 characters in the MP analy- nophyletic groups in all trees with high bootstrap val-ues (99–100%) (Fig. 2). Caprinae was defined by 7–9sis (Fig. 2), and occurred in a clade with Cervinae. The

Cervinae was defined by 4 characters and high boot- characters and Bovinae by 12–14 characters. Jukes-Cantor distances were also relatively high betweenstrap values (96–97%). The Odocoileinae was consis-

tently defined as monophyletic, although by only 1 or Bovinae and Caprinae and between Muntiacinae andthe other cervids (Table 2).

Below the subfamily level, our samples included fourTABLE 2 genera with more than one taxon. Two genera were

monophyletic (Ovis in Caprinae, Odocoileus in Odo-Jukes-Cantor (1969) Distances for the Fourth Exoncoileinae), and two were paraphyletic (Cervus and Ela-of K-Casein of Artiodactylsphurus in Cervinae and Bison and Bos in Bovinae).

Comparison Range Meana SD Within Odocoileinae, Odocoileus, Mazama, and Ran-gifer occur as lineages in a clade defined by two charac-Within subfamiliesters and bootstrap values of 77–79%, and CapreolusWithin Odocoileinae 0.0054–0.0473 0.0233 0.0124

Within Cervinae 0.0054–0.0275 0.0172 0.0093 and Alces occur in a clade defined by only one characterWithin Bovinae 0.0081–0.0109 0.0090 0.0016 and bootstrap values of 60–91%. Within Caprinae, Ore-Within Caprinae 0.0107–0.0589 0.0346 0.0129 amnos and Ovibos form a clade defined by two charac-Between subfamilies

ters and a bootstrap value of 70–77%, separate from aOdocoileinae–Cervinae 0.0387–0.0736 0.0485 0.0088Capra–Ovis clade, which is also defined by two charac-Odocoileinae–Muntiacinae 0.0916–0.1164 0.0982 0.0085

Cervinae–Muntiacinae 0.0886–0.1008 0.0937 0.0046 ters and bootstrap values of 68–88%. These four generaBovinae–Caprinae 0.0647–0.0886 0.0808 0.0070 in Caprinae share a 6-nucleotide insertion (Fig. 1) lack-

Between Pecoran families ing from all other taxa, including Saiga. Saiga has aCervidae–Bovidae 0.0706–0.1618 0.0975 0.0165large (36 nucleotides) insertion lacking from all otherBovidae–Antilocapridae 0.0677–0.0877 0.0820 0.0075

Cervidae–Antilocapridae 0.0707–0.1357 0.0863 0.0160 taxa (Fig. 1).Bovidae–Giraffidae 0.0706–0.0947 0.0833 0.0073 As shown with RFLP analysis of Bison and RangiferCervidae–Giraffidae 0.0589–0.1227 0.0742 0.0161 Κ-casein (Cronin and Cockett, 1993; Cronin et al.,Antilocapridae–Giraffidae — 0.0589 — 1995), we detected variation at the intraspecific levelTragulidae–Pecorab 0.1165–0.2031 0.1554 0.1754

in these taxa and C. elaphus with sequence analysis.Ruminants–Susb 0.2155–0.2881 0.2525 0.0161Subspecies of C. elaphus, Odocoileus hemionus, and B.

a Mean values were calculated as the mean of all pairwise distances bison appear paraphyletic relative to C. nippon, O. vir-among each group of taxa. ginianus, and Bos taurus, respectively. In the distanceb Pecora includes all taxa except Tragulidae and Sus, and rumi-

trees, B. b. athabascae occurs in a clade with Bos, sepa-nants include all taxa except Sus.

304 CRONIN ET AL.

Consensus

FIG. 2. Two maximum parsimony trees (MP1 and MP2) andstrict consensus tree resulting from phylogenetic analysis of Κ-caseinDNA sequence of artiodactyls. The numbers on the MP trees indicatethe numbers of characters defining branches. In cases where acceler-ated and delayed optimization of character-states resulted in differ-ent characters on branches, the numbers in parentheses are thosefor delayed optimization. The numbers on the consensus tree arebootstrap values. The nodes in MP1 and MP2 trees are lettered A–F and characters defining families are listed in Table 3.

rate from B. b. bison; while in the MP trees, B. b. bison orans; monophyly of the pecoran families and subfami-lies; either Giraffidae or Cervidae is the sister groupoccurs with Bos. C. e. elaphus, C. e. nelsoni, and C. nip-

pon occur as separate lineages, with Elaphurus as sis- of Bovidae; and Antilocapridae is a sister group to aBovidae–Cervidae–Giraffidae clade. This is in contrastter group in all trees. O. hemionus hemionus occurs in

a clade with O. virginianus, separate from O. h. sit- to morphology of extant and fossil forms which indi-cates Giraffidae is a sister group to a clade containingkensis in all trees.Antilocapridae and Cervidae (Leinders and Heintz,1980; Groves and Grubb, 1987; Janis and Scott, 1987)DISCUSSIONor a clade containing Antilocapridae and Bovidae (Stir-ton, 1944; Simpson, 1945; Romer, 1966; O’Gara andThe phylogenetic relationships of ruminant Κ-casein

suggest the following key points: monophyly of the pec- Matsen, 1975; Hamilton, 1978).


FIG. 3. FITCH and Neighbor-Joining (NJ) trees resulting from phylogenetic analysis of Jukes-Cantor distances of Κ-casein DNA se-quences of artiodactyls. The numbers on the NJ tree are bootstrap values.

Phylogenetic analyses of mtDNA sequences also give giraffids, separate from a bovid clade (Irwin et al.,1991). The view of Webb and Taylor (1980), with ancontrasting results at the family level. Sequences of mi-

tochondrial 12S and 16S ribosomal RNA genes indicate unresolved tetrachotomy of cervids, bovids, antilo-caprids, and giraffids, is still justified if Κ-casein anda clade containing bovids and antilocaprids, with cer-

vids and giraffids in separate clades (Gatesy et al., mtDNA are both considered.The cervid subfamilies, Cervinae, Odocoileinae, and1992), or an unresolved polychotomy of the four fami-

lies (Kraus and Miyamoto, 1991; Allard et al., 1992). Muntiacinae, have distinct Κ-casein lineages, as withmtDNA (Miyamoto et al., 1990; Cronin, 1991), repeti-However, the mitochondrial ribosomal RNA results are

consistent with monophyly of each family, particularly tive DNA (Lima-de-Faria et al., 1984), and allozymes(Baccus et al., 1983). Muntiacinae is particularly dis-Bovidae (Allard et al., 1992). In contrast, sequences of

the mitochondrial cytochrome b gene indicate a poly- tinct, with 25 characters defining its branch in the MPtrees and large Jukes-Cantor distances from other cer-phyletic clade containing antilocaprids, cervids, and

306 CRONIN ET AL.

FIG. 3—Continued

vids. Sequences of mitochondrial rRNA genes also indi- mtDNA data in which C. elaphus and C. unicolor occurtogether in a clade. The Κ-casein results are also consis-cate Muntiacinae as a distinct lineage in a clade with

Cervinae (Miyamoto et al., 1990). Muntjacs also exhibit tent with allozyme data which show close relationshipsof C. e. elaphus, C. e. nelsoni, and C. nippon (Baccus etextreme variation in chromosome number compared to

other cervids (Hsu and Benirschke, 1977; Goss, 1983). al., 1983; Emerson and Tate, 1993).Within Odocoileinae, the close relationship of Odo-Within Cervinae, Cervus appears to be a paraphy-

letic genus that encompasses Elaphurus with Κ-casein coileus and Mazama indicated by allozymes (Smith etal., 1986) and mtDNA (Cronin, 1991) is supported byresults, as with mtDNA (Cronin, 1991) and allozyme

(Emerson and Tate, 1993) results. These genera also the Κ-casein results. The clade containing Capreolusand Alces is not strongly supported in the MP trees [onehybridize readily (Tate et al., 1995). The Κ-casein re-

sults suggest a clade with C. elaphus, C. nippon, and character and a low bootstrap value (60%)], althoughthe distance analysis also grouped them together withElaphurus and another with C. unicolor and C. du-

vauceli. This agrees with the allozyme, but not the a high bootstrap value (91%). However, Capreolus is


TABLE 3

Characters Defining Family-Level Branches of Artiodactyl K-Casein Maximum Parsimony (MP) Trees (Fig. 2)

Character CharacterBranch in (sequence Consistency Branch in (sequence Consistency

Fig. 2 position) index Change Fig. 2 position) index Change

Node A–Node B Node B–Antilocapridae(MP1 and MP2) (MP1 and MP2)

4 1.000 C → T 6 1.000 G → C20 1.000 A → T 109 1.000 T → A96 1.000 C → T 126 1.000 C → G97 1.000 A → T 234 0.500 A → G

120 1.000 C → T 244 0.600 T → A143 1.000 A → C 278 1.000 A → T160 0.500 G → A 375 0.500 T → A275 0.333 T → C 392 1.000 A → C383 0.500 C → T386 1.000 A → G Node B–Node E (MP2)403 1.000 C → A 154a 0.500 G → A

262a 0.500 C → GNode B–Node C (MP1) 279 1.000 T → G

166a 0.333 A → G 376 0.333 C → T262 0.500 C → T 423 1.000 G → A279 1.000 T → G376 0.333 C → T Node E–Node F (MP2)423 1.000 G → A 166 0.500 A → G

262 0.500 G → TNode C–Node D (MP1)

154 1.000 G → A Node F–Cervidae (MP2)375a 0.500 T → G 55 1.000 T → G385a 0.500 C → A 83 1.000 T → C

188 0.667 A → GNode D–Cervidae (MP1) 249 1.000 C → T

55 1.000 T → G 288 0.500 A → G83 1.000 T → C 375 0.500 T → G

166b 0.333 A → G 385 0.500 C → A188 0.667 A → G 409 1.000 T → A249 1.000 C → T288 0.500 A → G Node F–Giraffidae (MP2)375b 0.500 T → G 13 0.500 T → C409 1.000 T → A 19 0.500 A → G

71 1.000 T → GNode D–Bovidae (MP1) 154 0.500 A → G

95 0.500 C → T 217 1.000 T → G166a 0.333 G → A 271 1.000 C → T215 1.000 C → A 284 1.000 A → T241 1.000 C → G 336 0.500 A → G244a 0.600 T → C 358 0.600 T → G262 0.500 T → G427a 0.667 T → A Node E–Bovidae (MP2)

95 0.500 C → TNode C–Giraffidae (MP1) 154 b 0.500 G → A

13 0.500 T → C 215 1.000 C → A19 0.500 A → G 241 1.000 C → G71 1.000 T → G 244a 0.600 T → C

166b 0.333 A → G 262 b 0.500 C → G217 1.000 T → G 427a 0.667 T → A271 1.000 C → T284 1.000 A → T336 0.500 A → G358 0.600 T → G

a These characters define branches only in analysis with accelerated optimization.b These characters define branches only in analysis with decelerated optimization.

308 CRONIN ET AL.

considerably differentiated from the other taxa, with overlap of sequence divergences between the inter- andintrafamily levels, which may reflect the rapid radia-nine characters defining its branch on the MP trees.

The occurrence of Rangifer in a clade with Odocoileus tions of the families and intrafamily lineages (Table 2;Allard et al., 1992).and Mazama is in contrast with the mtDNA data in

which Rangifer occurred in a clade independent of the Considering the estimated radiation of Bovidae, Cer-vidae, Antilocapridae, and Giraffidae 20–25 mybp inother Odocoileine taxa (Cronin, 1991). The close rela-

tionship of O. virginianus and O. hemionus is apparent the late Oligocene to early Miocene (Romer, 1966; Sav-age and Russell, 1983), our mean sequence divergencesfrom the Κ-casein data, in which O. virginianus (white-

tailed deer) is in a clade with O. h. hemionus (mule of these families (0.0589–0.0975, Table 2) suggest arate of Κ-casein exon evolution of 0.002–0.005 nucleo-deer), separate from O. h. sitkensis (black-tailed deer).

MtDNA data also depict O. hemionus as paraphyletic as tide substitutions per million years. This is about anorder of magnitude slower than mtDNA (Brown et al.,mule deer and white-tailed deer share similar mtDNA,

while black-tailed deer mtDNA is quite divergent (5– 1979). A rate of about 0.004 substitutions per millionyears for Κ-casein evolution is also supported by the7%) from them (Carr et al., 1986; Cronin et al., 1988).

Within the Bovidae, Bovinae and Caprinae each ap- mean sequence divergences (Table 2) of ruminants andSus (0.2525) which are thought to have diverged 60pear as monophyletic in our Κ-casein phylogeny as in

nuclear ribosomal DNA (Wall et al., 1992) and mtDNA mybp, Odocoileinae and Cervinae (0.0485) which di-verged about 10 mybp (Miyamoto et al., 1990), and the(Allard et al., 1992; Gatesy et al., 1992; Cronin, 1994)

phylogenies. The Κ-casein results show Ovibos, Ore- major bovid lineages (two of which are represented byour Caprinae and Bovinae, 0.0808) which originatedamnos, Saiga, and Capra/Ovis in separate clades

within Caprinae, consistent with the tribe status of between 16 and 28 mybp (Allard et al., 1992). WhereasmtDNA is generally useful from phylogenetic analysisthese taxa (Vaughan, 1978).

We identified different Κ-casein sequences in subspe- below the family level, the slower rate of evolution sug-gests that Κ-casein is useful for phylogenetic assess-cies of B. bison and paraphyly of the sequences with

those of Bos. Intraspecific variation of Κ-casein has ment at the family and subfamily levels or higher (Mer-cier et al., 1976; J. E. Gatesy unpublished manuscript).been detected in B. taurus (Gorodetskii and Kaledin,

1987; Pinder et al., 1991; Schlieben et al., 1991), B. bi- Paraphyly among genera, species, and subspecies sug-gests that Κ-casein gene trees should be used cau-son (Cronin and Cockett, 1993; Sipko et al., 1994), and

Bison bonasus (Burzynska and Topczewski, 1995). The tiously when inferring phylogenies at these levels.However, when considering allele frequency distribu-differences in Κ-casein sequence between B. b. bison

and B. b. athabascae do not indicate strict phylogenetic tions, Κ-casein is useful for assessing population ge-netic or breeding structure (Cronin and Cockett, 1993;divergence of the subspecies, as different alleles of Κ-

casein and other nuclear and mitochondrial loci are Cronin et al., 1995).For many vertebrates, systematic studies of geneshared by the subspecies and by Bison and Bos (Bork et

al., 1991; Cronin and Cockett, 1993; Udina et al., 1994; phylogenies have been restricted to a few loci, particu-larly mtDNA and nuclear ribosomal RNA genes (re-Polziehn et al., 1995).

Besides phylogeny, there are other interesting com- viewed by Avise, 1994). It is well-established that mul-tiple gene trees and intraspecific variation should beparisons of Κ-casein and mtDNA sequences. First, the

transition/transversion ratio is lower in Κ-casein (1.7) considered when using molecular data to infer speciesphylogenies (Pamilo and Nei, 1988; Cronin et al., 1991;than ribosomal RNA genes of mtDNA (2.8–4.8; Miya-

moto et al., 1990). Second, the sequence divergences of Powell, 1991; Cronin, 1993). This is particularly truefor closely related species which may share polymor-mtDNA (as estimated from restriction maps of the en-

tire mtDNA molecule; Cronin, 1991) are generally phic alleles from a common ancestor. Analyses of multi-ple genes, including mtDNA and single-copy nuclearhigher for mtDNA than Κ-casein (Table 2). For exam-

ple, the divergences within the subfamilies Odocoilei- DNA, are increasingly being combined in systematicanalyses (e.g., Slade et al., 1994). Κ-Casein may be anae or Cervinae are: 0.5–4.7% for Κ-casein and 4–12%

for mtDNA; between these subfamilies 3.8–7.4% for Κ- useful addition to the genes studied in mammalianphylogenetics.casein and 9–19% for mtDNA; and between Cervidae

and Bovidae 7.1–16.2% for Κ-casein and 14–20% formtDNA. An exception is that divergences of Κ-casein

ACKNOWLEDGMENTS(8.9–11.6%) are higher than that of ribosomal RNAmtDNA (5.6–7.9%) between Muntiacinae and either

We thank those listed in Table 1 who supplied tissues for thisCervinae or Odocoileinae (Miyamoto et al., 1990).study. G. Dragoo and J. Wickliffe provided invaluable help in labThese observations may reflect the overall relativelyanalyses. J. E. Gatesy generously provided insight and assistance inrapid rate of mtDNA evolution (Brown et al., 1979), but data analysis. A. Bishop, E. Brooks, and P. Kircher provided assis-

the conserved nature of ribosomal RNA mtDNA se- tance with manuscript preparation. M. Goodman and three anony-mous reviewers provided useful comments on the manuscript.quences. Third, for both mtDNA and Κ-casein, there is


tion fragment length polymorphism in mitochondrial DNA of sheepREFERENCESand goats. J. Anim. Sci. 72: 796.

Cronin, M. A., and Cockett, N. (1993). Kappa-casein polymorphismsAlexander, L. J., Stewart, A. F., Mackinlay, A. G., Kapelinskaya,among cattle breeds and bison herds. Anim. Genet. 24: 135–138.T. V., Tkach, T. M., and Gorodetsky, S. I. (1988). Isolation and char-

Cronin, M. A., Amstrup, S. C., Garner, G. W., and Vyse, E. R. (1991).acterization of the bovine Κ-casein gene. Eur. J. Biochem. 178:Interspecific and intraspecific mitochondrial DNA variation in395–401.North American bears (Ursus). Can. J. Zool. 69: 2985–2992.Allard, M. W., Miyamoto, M. M., Jarecki, L., Kraus, F., and Tennant,

Cronin, M. A., Renecker, L., Pierson, B. J., and Patton, J. C. (1995).M. R. (1992). DNA systematics and evolution of the artiodactylGenetic variation in domestic reindeer and wild caribou in Alaska.family Bovidae. Proc. Natl. Acad. Sci. USA 89: 3972–3976.Anim. Genet. 26: 427–434.Avise, J. C. (1994). ‘‘Molecular Markers, Natural History and Evolu-

Cronin, M. A., Vyse, E. R., and Cameron, D. G. (1988). Genetic rela-tion,’’ Chapman & Hall, New York.tionships between mule deer and white-tailed deer in Montana. J.Baccus, R., Ryman, N., Smith, M. H., Reuterwall, C., and Cameron,Wildl. Manage. 52: 320–328.D. G. (1983). Genetic variability and differentiation of large graz-

Doolittle, R. F., Schubert, D., and Schwartz, S. A. (1967). Amino aciding mammals. J. Mamm. 64: 109–120.sequence studies on artiodactyl fibrinopeptides. I. dromedaryBeintema, J. J., Fitch, W. M., and Carsana, A. (1986). Molecular evo-camel, mule deer, and cape buffalo. Arch. Biochem. Biophys. 118:lution of pancreatic-type ribonucleases. Mol. Biol. Evol. 3: 262–456–467.275.

Emerson, B. C., and Tate, M. L. (1993). Genetic analysis of evolution-Beintema, J. J., Schuller, C., Irie, M., and Carsana, A. (1988). Molec-ary relationships among deer (subfamily Cervinae). J. Hered. 84:ular evolution of the ribonuclease superfamily. Prog. Biophys. Mol.266–273.Biol. 51: 165–192.

Felsenstein, J. (1985). Confidence limits on phylogenies: An approachBishop, M. D., Kappes, S. M., Keele, J. W., Stone, R. T., Sunden, using the bootstrap. Evolution 39: 783–781.

S. L. F., Hawkins, G. A., Toldo, S. S., Fries, R., Grosz, M. D., Yoo,Felsenstein, J. (1993). PHYLIP—Phylogeny Inference PackageJ., and Beattie, C. W. (1994). A genetic linkage map for cattle. Ge-

(Vers. 3.2.) Cladistics 5: 164–166.netics 136: 619–639.Fitch, W. M., and Margoliash, E. (1967). Construction of phylogeneticBork, A. M., Strobeck, C. M., Yeh, F. C., Hudson, R. J., and Salmon,

trees. Science 155: 279–284.R. K. (1991). Genetic relationship of wood and plains bison basedon restriction fragment length polymorphisms. Can. J. Zool. 69: Fries, R., Eggen, A., and Womack, J. E. (1993). The bovine genome43–48. map. Mamm. Genome 4: 405–428.

Furet, J. P., Mercier, J. C., Soulier, S., Gaye, P., Hue-Delahaie, D.,Brignon, G., Chtourou, A., and Ribadeau-Dumas, B. (1985). Prepara-and Vilotte, J. L. (1990). Nucleotide sequence of ovine Κ-caseintion and amino acid sequence of human Κ-casein. FEBS Lett. 188:cDNA. Nucleic Acids Res. 18: 5286.48–54.

Gallagher, D. S., Jr., Derr, J. N., and Womack, J. E. (1994). Chromo-Brown, W. M., George, M., Jr., and Wilson, A. C. (1979). Rapid evolu-some conservation among the advanced pecorans and determina-tion of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA 76:tion of the primitive bovid karyotype. J. Hered. 85: 204–210.1967–1971.

Gatesy, J., Yelon, D., DeSalle, R., and Vrba, E. S. (1992). PhylogenyBubenik, A. B. (1990). Epigenetical, morphological, physiological,of the Bovidae (Artiodactyla, Mammalia), based on mitochondrialand behavioral aspects of evolution of horns, pronghorns, and ant-ribosomal DNA sequences. Mol. Biol. Evol. 9: 433–446.lers. In ‘‘Horns, Pronghorns, and Antlers’’ (G. A. Bubenik and A. B.

Bubenik, Eds.), pp. 3–113, Springer-Verlag, New York. Geist, V. (1982). Adaptive behavioral strategies. In ‘‘Elk of NorthAmerica’’ (J. W. Thomas and D. E. Toweill, Eds.), pp. 219–277,Burzynska, B., and Topczewski, J. (1995). Genotyping of Bison bona-Stackpole Books, Harrisburg, PA.sus Κ-casein gene following DNA sequence amplification. Anim.

Genet. 26: 335–336. Geist, V. (1987). On speciation in Ice Age mammals, with special ref-erence to cervids and caprids. Can. J. Zool. 65: 1067–1084.Coll, A., Folch, M., and Sanchez, A. (1993). Nucleotide sequence of

the goat Κ-casein cDNA. J. Anim. Sci. 71: 2833. Georgiadis, N. J., Kat, P. W., Oketch, H., and Patton, J. (1990). Allo-zyme divergence within the Bovidae. Evolution 44: 2135–2149.Carr, S. M., and Marshall, H. D. (1991). Detection of intraspecific

DNA sequence variation in the mitochondrial cytochrome b gene Gorodetskii, S. I., and Kaledin, A. S. (1987). Analysis of nucleotideof Atlantic cod (Gadus morhua) by the polymerase chain reaction. sequence of bovine kappa-casein cDNA. Genetika 23: 398–404.Can. J. Fish. Aquat. Sci. 48: 48–52. Goss, R. J. (1983). ‘‘Deer Antlers: Regeneration, Function, and Evolu-

Carr, S. M., Ballinger, S. W., Derr, J. N., Blankenship, H., and Bick- tion,’’ Academic Press, New York.ham, J. W. (1986). Mitochondrial DNA analysis of hybridization Gould, S. J. (1974). The origin and function of ‘‘bizarre’’ structures:between sympatric white-tailed deer and mule deer in West Texas. Antler size and skull size in the ‘‘Irish elk,’’ Megaloceros giganteus.Proc. Natl. Acad. Sci. USA 83: 9576–9580. Evolution 28: 191–220.

Crabtree, G. R., Comeau, C. M., Fowlkes, D. M., Fornace, A. J., Mal- Graur, D., and Higgins, D. G. (1994). Molecular evidence for the in-ley, J. D., and Kant, J. A. (1985). Evolution and structure of the clusion of cetaceans within the order Artiodactyla. Mol. Biol. Evol.fibrinogen genes. J. Mol. Biol. 185: 1–19. 11: 357–364.

Cronin, M. A. (1989). ‘‘Molecular Evolutionary Genetics and Phylog- Grosclaude, F., Mercier, J. C., and Ribadeau Dumas, B. (1973). Ge-eny of Cervids.’’ Ph.D. dissertation, Yale University, New Haven, netic aspects of cattle casein research. Netherlands Milk Dairy J.CT. 27: 328–340.

Cronin, M. A. (1991). Mitochondrial-DNA phylogeny of deer (Cervi- Groves, C. P., and Grubb, P. (1987). Relationships of living deer. Indae). J. Mamm. 72: 533–566. ‘‘Biology and Management of the Cervidae’’ (C. Wemmer, Ed.), pp.

Cronin, M. A. (1993). Mitochondrial DNA in wildlife taxonomy and 21–59, Smithsonian Inst. Press, Washington, DC.conservation biology: cautionary notes. Wildl. Soc. Bull. 21: 339– Gustafson, E. P. (1985). Antlers of Bretzia and Odocoileus (Mam-348. malia, Cervidae) and the evolution of New World deer. Trans. Ne-

braska Acad. Sci., 13: 83–92.Cronin, M. A. (1994). Rapid communication: A unique SacII restric-

310 CRONIN ET AL.

Guthrie, R. D. (1984). Alaskan megabucks, megabulls, and mega- Miyamoto, M. M., Kraus, F., and Ryder, O. A. (1990). Phylogeny andevolution of antlered deer determined from mitochondrial DNA se-rams: the issue of Pleistocene gigantism. In ‘‘Contributions in

Quaternary Vertebrate Paleontology,’’ No. 8, Spec. Publ., (H. H. quences. Proc. Natl. Acad. Sci. USA 87: 6127–6131.Genoways and M. R. Dawson, Eds.), pp. 482–510, Carnegie Mu- Mross, G. A., and Doolittle, R. F. (1967). Amino acid sequence studiesseum of Natural History, Pittsburgh, PA. on artiodactyl fibrinopeptides II. Vicuna, elk, muntjak, pronghorn

antelope, and water buffalo. Arch. Biochem. Biophys. 122: 674–Hamilton, W. R. (1978). Fossil giraffes from the Miocene of Africa,684.and a revision of the Phylogeny of the Giraffoidea. Trans. R. Soc.,

London Ser. B. 283: 165–229. Mullis, K., and Faloona, F. (1987). Specific synthesis of DNA in vitrovia a polymerase catalyzed chain reaction. Methods Enzymol. 155:Hendy, M. D., and Penny, D. (1982). Branch and bound algorithms335–350.to determine minimal evolutionary trees. Math. Biosci. 59: 277–

290. Nakhasi, H. L., Grantham, F. H., and Gullino, P. M. (1984). Expres-sion of Κ-casein in normal and neoplastic rat mammary gland isHonacki, J. H., Kinman, K. E., and Koeppl, J. S. (1982). ‘‘Mammalunder the control of Prolactin. J. Biol. Chem. 259: 14894–14898.Species of the World,’’ Allen Press, Lawrence, KS.

Nowak, R. M., and Paradiso, J. L. (1983). ‘‘Walker’s Mammals of theHsu, T. C., and Benirschke, K. (1977). ‘‘An Atlas of Mammalian Chro-World,’’ Johns Hopkins Univ. Press, Baltimore, MD.mosomes.’’ Vol. 10, Folios 451–517, Springer-Verlag, Berlin/New

York. O’Gara, B. W., and Matsen, G. (1975). Growth and casting of hornsby pronghorns and exfoliation of horns by bovids. J. Mamm. 56:Irwin, D. M., Kocher, T. D., and Wilson, A. C. (1991). Evolution of829–846.cytochrome b gene of mammals. J. Mol. Evol. 32: 128–144.

Pamilo, P., and Nei, M. (1988). Relationships between gene trees andIrwin, D. M., Prager, E. M., and Wilson, A. C. (1992). Evolutionaryspecies trees. Mol. Biol. Evol. 5: 568–583.genetics of ruminant lysozymes. Anim. Genet. 23: 193–202.

Philippe, H., and Douzery, E. (1994). The pitfalls of molecular phylog-Irwin, D. M., White, R. T., and Wilson, A. C. (1993). Characterizationeny based on four species, as illustrated by the Cetacea/Artiodac-of the cow stomach lysozyme genes: repetitive DNA and concertedtyla relationships. J. Mamm. Evol. 2: 133–153.evolution. J. Mol. Evol. 37: 355–366.

Pinder, S. J., Perry, B. N., Skidmore, C. J., and Savva, D. (1991).Janis, C. M. (1988). New ideas in ungulate phylogeny and evolution.Analysis of polymorphism in the bovine casein genes by use of theTrends Ecol. Evol. 3: 291–297.polymerase chain reaction. Anim. Genet. 22: 11–20.Janis, C. M., and Scott, K. M. (1987). The inter-relationships of

Polziehn, R. O., Strobeck, C., Sheraton, J., and Beech, R. (1995). Bo-higher ruminant families with special emphasis on the membersvine mitochondrial DNA discovered in North American bison popu-of the Cervoidea. Am. Mus. Novitates 2893: 1–85.lations. Cons. Biol. 9: 1638–1643.Jolles, P., Loucheux-Lefebvre, M.-H., and Henschen, A. (1978). Struc-

Powell, J. R. (1991). Monophyly/paraphyly/polyphyly and gene/spe-tural relatedness of Κ-casein and fibrinogen γ-chain. J. Mol. Evol.cies trees: An example from Drosophila. Mol. Biol. Evol. 8: 892–11: 271–277.896.Jukes, T. H., and Cantor, C. R. (1969). Evolution of protein molecules.

Rohrer, G. A., Alexander, L. J., Keele, J. W., Smith, T. P., and Beattie,In ‘‘Mammalian Protein Metabolism’’ (H. N. Munro, Ed.), pp. 21–C. W. (1994). A microsatellite linkage map of the porcine genome.132, Academic Press, New York.Genetics 136: 231–245.Kraus, F., and Miyamoto, M. M. (1991). Rapid cladogenesis among

Romer, A. S. (1966). ‘‘Vertebrate Paleontology,’’ Univ. of Chicagothe pecoran ruminants: evidence from mitochondrial DNA se-Press, Chicago, Illinois.quences. Syst. Zool. 40: 117–130.

Saitou, N., and Nei, M. (1987). The neighbor-joining method: A newKraus, F., Jarecki, L., Miyamoto, M. M., Tanhauser, S. M., andmethod for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:Laipis, P. J. (1992). Mispairing and compensational changes dur-406–425.ing the evolution of mitochondrial ribosomal RNA. Mol. Biol. Evol.

9: 770–774. Savage, D. E., and Russell, D. E. (1983). ‘‘Mammalian Paleofaunasof the World,’’ Addison–Wesley, London.Kimura, M. (1980). A simple method for estimating evolutionary rate

of base substitutions through comparative studies of nucleotide se- Schaar, J., Hansson, B., and Pettersson, H. (1985). Effects of geneticquences. J. Mol. Evol. 16: 111–120. variants of Κ-casein and b-lactoglobulin on cheesemaking. J. Dairy

Res. 52: 429–437.Kumar, S., Tamura, K., and Nei, M. (1993). ‘‘MEGA: Molecular Evo-lutionary Genetics Analysis, version 1.01,’’ Pennsylvania State Schlieben, S., Erhardt, G., and Senft, B. (1991). Genotyping of bovineUniv., University Park, PA. Κ-casein (Κ-CNA, Κ-CNB, Κ-CNC, Κ-CNE) following DNA sequence

amplification and direct sequencing of Κ-CNE PCR product. Anim.Leinders, J. J. M., and Heintz, E. (1980). The configuration of theGenet. 22: 333–342.lacrimal orifice in pecorans and tragulinds (Artiodactyla: Mam-

malia) and its significance for the distinction between Bovidae and Simpson, G. G. (1945). The principles of classification, and a classifi-Cervidae. Beaufortia 30: 155–160. cation of mammals. Bull. Am. Mus. Nat. Hist. 85.

Levine, W. B., Alexander, L. J., Hoganson, G. E., and Beattie, C. W. Sipko, T. P., Udina, I. G., Badagueva, Y. N., and Sulimova, G. E.(1992). Cloning and sequencing of the porcine Κ-casein cDNA. (1994). Polymorphism of kappa-casein gene in the family Bovidae:Anim. Genet. 23: 361–363. Comparative analysis. Genetika 30: 225–229.

Lima-de-Faria, A., Arnason, U., Widegren, B., Essen-Moller, J., Slade, R. W., Moritz, C., and Heideman, A. (1994). Multiple nuclear-Isaksson, M., Olsson, E., and Jaworska, H. (1984). Conservation gene phylogenies: application to pinnipeds and comparison with aof repetitive DNA sequences in deer species studied by Southern mitochondrial DNA gene phylogeny. Mol. Biol. Evol. 11: 341–356.blot transfer. J. Mol. Evol. 20: 17–24. Smith, M. H., Branan, W. V., Marchinton, R. L., Johns, P. E., and

Meester, J., and Setzer, H. W. (1971). ‘‘The Mammals of Africa. An Wooten, M. C. (1986). Genetic and morphologic comparisons of redIdentification Manual’’ (as revised 1977). Smithson. Inst. Press, brocket, brown brocket, and white-tailed deer. J. Mamm. 67: 103–Washington, DC. 111.

Stewart, A. F., Willis, I. M., and Mackinlay, A. G. (1984). NucleotideMercier, J. C., Chobert, J. M., and Addeo, F. (1976). Comparativestudy of the amino acid sequences of the Caseinomacropeptides sequences of αs1- and Κ-casein cDNAs. In ‘‘Nucleic Acids Research,’’

pp. 3895–3907, IRL Press, Oxford, England.from seven species. FEBS Lett. 72: 208–214.


Stirton, R. A. (1944). Comments on the relationships of the Palaeo- to an endogenous type C RNA virus of Odocoileus hemionus. J.Virol. 23: 1–9.merycidae. Am. J. Sci. 242: 633–655.

Swofford, D. L. (1993). ‘‘Phylogenetic Analysis Using Parsimony,’’ Udina, I. G., Sokolova, S. S., Sipko, T. P., and Sulimova, G. E. (1994).Center for Biodiversity, Illinois Natural History Survey, Cham- Comparative analysis of polymorphism for DQB and DRB DNA locipaign, IL. of the major histocompatibility complex in representatives of fam-

ily Bovidae. Russ. J. Genet. 30: 313–317.Swofford, D. L., and Olsen, G. J. (1990). Phylogeny reconstruction.In ‘‘Molecular Systematics’’ (D. M. Hillis and C. Moritz, Eds.), Vaughan, T. A. (1978). ‘‘Mammalogy,’’ Saunders, Philadelphia, PA.Chap. 11, pp. 411–500, Sinauer, Sunderland, MA. Vrba, E. S. (1987). Ecology in relation to speciation rates: some case

histories of Miocene—Recent mammal clades. Evol. Ecol. 1: 283–Tate, M. L., Mathias, H. C., Fennessy, P. F., Dodds, K. G., Penty,J. M., and Hill, D. F. (1995). A new gene mapping resource: Inter- 300.species hybrids between Pere David’s deer (Elaphurus davidianus) Wall, D. A., Davis, S. K., and Read, B. M. (1992). Phylogenetic rela-and red deer (Cervus elaphus). Genetics 139: 1383–1391. tionships in the subfamily Bovinae (Mammalia: artiodactyla)

based on ribosomal DNA. J. Mamm. 73: 262–275.Thompson, M. D., Dave, J. R., and Nakhasi, H. L. (1985). Molecularcloning of mouse mammary gland Κ-casein: Comparison with rat Webb, S. D., and Taylor, B. E. (1980). The phylogeny of hornless ru-Κ-casein and rat and human γ-fibrinogen. DNA 4: 263–271. minants and a description of the cranium of Archaeomeryx. Bull.

Am. Mus. Nat. Hist. 167: 117–158.Todd, N. B. (1975). Chromosomal mechanisms in the evolution of ar-tiodactyls. Paleobiology 1: 175–188. Wilson, A. C., Maxson, L. R., and Sarich, V. M. (1974). Two types of

molecular evolution. Evidence from studies of interspecific hybrid-Tronick, S. R., Golub, M. M., Stephenson, J. R., and Aaronson, S. A.(1977). Distribution and expression in mammals of genes related ization. Proc. Nat. Acad. Sci. USA 71: 2843–2847.

k-casein gene phylogeny of higher ruminants (pecora, artiodactyla)

Documents