Mitochondrial DNA phylogeography of red deer (Cervus elaphus)

In order to understand the origin, phylogeny, and phylogeography of the species Cervus elaphus, we examined the DNA sequence variation of the mitochondrial cytochrome b gene of 51 populations of deer from the entire distribution area of Cervinae with an emphasis on Europe and Asia. Several methods, including maximum parsimony, maximum likelihood, and nested clade analysis, revealed that red deer originated from the area between Kyrgyzstan and Northern India. We found two distinct groups of red deer: a western group consisting of four subgroups and an eastern group consisting of three subgroups. Our mtDNA data do not support the traditional classification of red deer as only one species nor its division into numerous subspecies. The discrepancies between the geographical pattern of differentiation based on mtDNA cytochrome b and the existing specific and subspecific taxonomy based on morphology are discussed.     

Phylogeny and classification of the Old World Emberizini (Aves, Passeriformes)

The phylogeny of the avian genus Emberiza and the monotypic genera Latoucheornis, Melophus and Miliaria (collectively the Old World Emberizini), as well as representatives for the New World Emberizini, the circumpolar genera Calcarius and Plectrophenax and the four other generally recognized tribes in the subfamily Emberizinae was estimated based on the mitochondrial cytochrome b gene and introns 6-7 of the nuclear ornithine decarboxylase (ODC) gene. Our results support monophyly of the Old World Emberizini, but do not corroborate a sister relationship to the New World Emberizini. Calcarius and Plectrophenax form a clade separated from the other Emberizini. This agrees with previous studies, and we recommend the use of the name Calcariini. Latoucheornis, Melophus and Miliaria are nested within Emberiza, and we therefore propose they be synonymized with Emberiza. Emberiza is divided into four main clades, whose relative positions are uncertain, although a sister relation between a clade with six African species and one comprising the rest of the species (30, all Palearctic) is most likely. Most clades agree with traditional, morphology-based, classifications. However, four sister relationships within Emberiza, three of which involve the previously recognized Latoucheornis, Melophus and Miliaria, are unpredicted, and reveal cases of strong morphological divergence. In contrast, the plumage similarity between adult male Emberiza (formerly Latoucheornis) siemsseni and the nominate subspecies of the New World Junco hyemalis is shown to be the result of parallel evolution. A further case of parallel plumage evolution, between African and Eurasian taxa, is pointed out. Two cases of discordance between the mitochondrial and nuclear data with respect to branch lengths and genetic divergences are considered to be the result of introgressive hybridization.     

A phylogenetic analysis of the palm subtribe Oncospermatinae (Arecaceae) based on morphological characters

Subtribe Oncospermatinae (Arecaceae: Arecoideae: Areceae) is a diverse group of spiny Old World palms. The subtribe includesOncosperma, a widespread Asian genus of five species, along with seven monotypic genera, all endemic to the Seychelles and Mascarene Islands of the western Indian Ocean. A phylogenetic analysis was conducted in order to test the monophyly of subtribe Oncospermatinae with respect to other Old World genera of tribe Areceae. A matrix of 38 morphological characters was scored for 29 taxa, including 11 species of the Oncospermatinae. A single most parsimonious tree was found, resolving the subtribe as a polyphyletic group of two distinct clades. One clade containingAcanthophoenix, Deckenia, Oncosperma, andTectiphiala was placed as sister to a large group that includes members of subtribes Archontophoenicinae, Arecinae, Iguanurinae, and Ptychospermatinae. The other clade of Oncospermatinae, including the Seychelles endemic generaNephrosperma, Phoenicophorium, Roscheria, andVerschaffeltia, was resolved as sister to the Madagascar endemic subtribe Masoalinae, and may have arisen in the western Indian Ocean region.     

Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity

Old World leaf-nosed bats (Hipposideridae) are among the most widespread and ecologically diverse groups of insectivorous bats in the Old World tropics. However, phylogenetic relationships in Hipposideridae are poorly resolved at both the generic and species levels, and deep genetic divergence within several Southeast Asian species suggests that current taxonomy underestimates hipposiderid diversity in this region. We used mitochondrial and nuclear sequence data to conduct the first extensive molecular phylogenetic analysis of Southeast Asian hipposiderid bats. Inclusion of multiple samples per taxon allowed testing for evidence of evolutionarily distinct lineages within taxa currently defined as single species. In contrast to earlier phylogenies based on morphometrics, molecular data support monophyly of Hipposideros, but are ambiguous regarding the monophyly of Hipposideridae. With a few exceptions, molecular data also support currently recognized species groups classified by qualitative morphological characters. Widespread paraphyly and polyphyly within many currently recognized species of Hipposideros indicates that evolutionary diversity in the genus is underrepresented by current nomenclature. Comparison of available morphological and echolocation data suggest that both geographic isolation and ecological selection have contributed to the diversification of Southeast Asian hipposiderid bats.     

Molecular systematics and biogeography of Resedaceae based on ITS and trnL-F sequences

The Resedaceae, containing 6 genera and ca. 85 species, are widely distributed in the Old World, with a major center of species diversity in the Mediterranean basin. Phylogenetic analyses of ITS and plastid trnL-trnF sequences of 66 species from all genera of the Resedaceae reveal (1) monophyly of the family, in congruence with preliminary phylogenetic studies; (2) molecular support for the traditional morphological subdivision of the Resedaceae into three tribes according to ovary and placentation types, and carpel number; (3) two monophyletic genera (Caylusea, Sesamoides), and one natural group (core Reseda), which includes the remaining four genera of the family (Ochradenus, Oligomeris, Randonia, Reseda); (4) a monophyletic origin for four of the six taxonomic sections recognized within Reseda (Leucoreseda, Luteola, Glaucoreseda, Phyteuma). Our results lead us to interpret an increment of the basic chromosome number in the family from x=5 to x=6 in at least two independent instances, and a broad representation of polyploids in multiple lineages across phylogenies, including association between octoploids and alien invasion in many parts of the world. Species diversity, endemism number, phylogenetic relationships and sequence divergence in Resedaceae suggest two major centers of differentiation, one in the western Mediterranean, and the other in the eastern Mediterranean and SW Asia. Two independent colonization events to the Canary Islands from Africa are indicated for the two Canarian Reseda endemics.     

The genus Cervus in eastern Eurasia

In 2004, Christian Pitra and co-workers published the first molecular phylogeny of Old World deer which advanced our understanding of the Cervinae immeasurably by demonstrating the non-monophyletic status of the red deer/wapiti group, the chital/hog deer group and the swamp deer/Eld's deer group. Therefore, many conspicuous external features—antler complexity, mane and rump-patch development—turned out to be related not to phylogeny as much as to climatic-related lifestyle factors. At a lower level, molecular genetics has reinforced some conclusions drawn on the basis of morphology or behaviour. Striking examples are the divisions between mainland and Japanese sika and between northern and southern forms of Japanese sika. In this paper, I will look at the species living in what Pitra et al. (Evolution and phylogeny of old world deer. Mol Phylogenet Evol 33:880–895, 2004) identified as the heartland of cervine evolution: eastern Eurasia. I will consider the two species groups in this region that seem to crystallize both the problems of cervine classification and the ways in which the new sources of evidence have opened up new avenues of inquiry.     

Y-chromosome Data and Tribal Affiliations of Allenopithecus and Miopithecus

The phylogeny of Old World monkeys has remained unresolved in part because of a lack of resolution in the Cercopithecinae. Competing morphological hypotheses have had Allen's swamp monkey (Allenopithecus nigroviridis) and the talapoins (Miopithecus spp.) as basal branches of either the tribe Cercopithecini or the tribe Papionini. Previous molecular analyses have not adequately addressed the issue. To better understand the evolutionary history of these primates, we sequenced and subjected to phylogenetic analysis 3.1 kb of 2 loci (TSPY and SRY) from the non-recombining portion of the Y-chromosome. Individuals from the genera Allenopithecus, Miopithecus, Erythrocebus, Chlorocebus, and Cercopithecus were surveyed and their sequences compared with those previously published for the Papionini and Colobinae. The results suggest Allenopithecus and Miopithecus are more closely related to the Cercopithecini than Papionini. Our data also support the hypothesis that within the Cercopithecini, Erythrocebus and Chlorocebus share a close evolutionary relationship, distinct from the other members of the tribe.     

Implications ofrbcL sequence data for higher order relationships of theLoasaceae and the anomalous aquatic plantHydrostachys (Hydrostachyaceae)

Subclass and ordinal relationships ofLoasaceae, a small predominately New World family, are examined usingrbcL sequence data. Sequences were examined for eight of the fifteen genera of theLoasaceae and the morphologically anomalous aquatic genusHydrostachys (Hydrostachyaceae). Parsimony analyses of these sequences, combined with previously publishedrcbL data, indicate thatLoasaceae belong in theCornales, and are the sister group ofHydrangeaceae. This agrees with phylogenies based on chloroplast DNA inverted repeat restriction site, morphological and chemical data. TherbcL trees support the monophyly of theLoasaceae and most generic relationships correspond to current subfamily divisions. TherbcL phylogeny also provides the first suggestion thatHydrostachys is allied with theHydrangeaceae in theCornales.     

New phylogenetic perspectives on the Cervidae (Artiodactyla) are provided by the mitochondrial cytochrome b gene.

The entire mitochondrial cytochrome b (cyt b) gene was compared for 11 species of the artiodactyl family Cervidae, representing all living subfamilies, i.e., the antlered Cervinae (Cervus elaphus, C. nippon, Dama dama), Muntiacinae (Muntiacus reevesi), and Odocoileinae (Odocoileus hemionus, Mazama sp., Capreolus capreolus, C. pygargus, Rangifer tarandus, Alces alces); and the antlerless Hydropotinae (Hydropotes inermis). Phylogenetic analyses using Tragulidae, Antilocapridae, Giraffidae and Bovidae as outgroups provide evidence for three multifurcating principal clades within the monophyletic family Cervidae. First, Cervinae and Muntiacus are joined in a moderately-to-strongly supported clade of Eurasian species. Second, Old World Odocoileinae (Capreolus and Hydropotes) associate with the Holarctic Alces. Third, New World Odocoileinae (Mazama and Odocoileus) cluster with the Holarctic Rangifer. The combination of mitochondrial cyt b and nuclear k-casein sequences increases the robustness of these three clades. The Odocoileini + Rangiferini clade is unambiguously supported by a unique derived cranial feature, the expansion of the vomer which divides the choana. Contrasting with current taxonomy, Hydropotes is not the sister group of all the antlered deers, but it is nested within the Odocoileinae. Therefore, Hydropotes lost the antlers secondarily. Thus, the mitochondrial cyt b phylogeny splits Cervidae according to plesiometacarpal (Cervinae + Muntiacinae) versus telemetacarpal (Odocoileinae + Hydropotinae) conditions, and suggests paraphyly of antlered deer.     

Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): Systematics, morphology, and biogeography

The family Cervidae includes 40 species of deer distributed throughout the northern hemisphere, as well as in South America and Southeast Asia. Here, we examine the phylogeny of this family by analyzing two mitochondrial protein-coding genes and two nuclear introns for 25 species of deer representing most of the taxonomic diversity of the family. Our results provide strong support for intergeneric relationships. To reconcile taxonomy and phylogeny, we propose a new classification where the family Cervidae is divided in two subfamilies and five tribes. The subfamily Cervinae is composed of two tribes: the tribe Cervini groups the genera Cervus, Axis, Dama, and Rucervus, with the Père David's deer (Elaphurus davidianus) included in the genus Cervus, and the swamp deer (Cervus duvauceli) placed in the genus Rucervus; the tribe Muntiacini contains Muntiacus and Elaphodus. The subfamily Capreolinae consists of the tribes Capreolini (Capreolus and Hydropotes), Alceini (Alces), and Odocoileini (Rangifer + American genera). Deer endemic to the New World fall in two biogeographic lineages: the first one groups Odocoileus and Mazama americana and is distributed in North, Central, and South America, whereas the second one is composed of South American species only and includes Mazama gouazoubira. This implies that the genus Mazama is not a valid taxon. Molecular dating suggests that the family originated and radiated in central Asia during the Late Miocene, and that Odocoileini dispersed to North America during the Miocene/Pliocene boundary, and underwent an adaptive radiation in South America after their Pliocene dispersal across the Isthmus of Panama. Our phylogenetic inferences show that the evolution of secondary sexual characters (antlers, tusk-like upper canines, and body size) has been strongly influenced by changes in habitat and behaviour.     

Chloroplast DNA restriction site variation in theVernonieae (Asteraceae), an initial appraisal of the relationship of New and Old World taxa and the monophyly ofVernonia

Chloroplast DNA restriction site variation was examined for 35 taxa in theVernonieae and four outgroup tribes, using 17 restriction enzymes mapped for ca. 900 restriction sites per species; 139 mutations were found to be phylogenetically informative. Phylogenetic trees were constructed using Wagner and weighted parsimony, and evaluated by bootstrap and decay analyses. Relationships of Old and New World taxa indicate complex geographical relationships; there was no clear geographic separation by hemisphere. The relationships between Old and New World Vernonias found here support prior morphological analyses. The sister group to all New and most Old World taxa was composed of a small group of Old World species including yellow-flowered, trinervate-leaved species previously postulated to be basal in the tribe. The majority of both New and Old World taxa are derived from a lineage beginning with the monotypic genusStokesia, an endemic of the southeastern United States. The genusVernonia was also found to be paraphyletic within both the New and Old World. Available data do not support either the separation ofVernonia or the tribeVernonieae into geographically distinct lineages. The pattern of relationships within theVernonieae for taxa from North America, Asia, Africa, Central and South America is most similar to that of several other groups of both plants and animals with a boreotropical origin, rather than an origin in Gondwanaland. Such a pattern of distribution suggests more ancient vicariant events than are routinely postulated for theAsteraceae.     

The mitochondrial control region of Cervidae: evolutionary patterns and phylogenetic content

The mitochondrial control region (CR) sequence, also known as the D- loop, has been determined for six Cervidae (Artiodactyla, Ruminantia): the red and fallow deers (subfamily Cervinae), the brocket deer and two roe deers (subfamily Odocoileinae), and the Chinese water deer (Hydropotinae). These new sequences have been aligned with available cervid and bovid orthologues. Comparative analyses indicate that the 5'- peripheral domain exhibits a 75-bp length polymorphism near sequences associated with the termination of the H-strand replication. The New World Odocoileinae possess the longest cervid CR due to the presence of an additional 47-bp tandem repeat, located in the 3'-peripheral domain, downstream of the initiation site for H-strand replication (OH) and the first conserved sequence block (CSB-1). This insertion represents a duplication spanning the OH to CSB-1 region and constitutes an exclusive synapomorphy for New World Odocoileinae. Phylogenetic analyses of the complete CR support the paraphyly of antlered deers due to the nesting of the antlerless Hydropotes within Odocoileinae. Capreolus is the closest relative of Hydropotes, and the divergence of this Old World Odocoileinae clade may have occurred between 8.7 and 10.4 MYA. The conserved central domain of CR can be aligned across ungulates and indicates the Pecora monophyly, their close association with cetaceans, and the earlier emergence of suiformes.      

Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Celastreae, which includes about 350 species of trees and shrubs in 15 genera, was inferred in a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (matK, trnL-F) genes. A strong correlation was found between the geography of the species sampled and their inferred relationships. Species of Maytenus and Gymnosporia from different regions were resolved as polyphyletic groups. Maytenus was resolved in three lineages (New World, African, and Austral-Pacific), while Gymnosporia was resolved in two lineages (New World and Old World). Putterlickia was resolved as nested within the Old World Gymnosporia. Catha edulis (qat, khat) was resolved as sister to the clade of Allocassine, Cassine, Lauridia, and Maurocenia. Gymnosporia cassinoides, which is reportedly chewed as a stimulant in the Canary Islands, was resolved as a derived member of Gymnosporia and is more closely related to Lydenburgia and Putterlickia than it is to Catha. Therefore, all eight of these genera are candidates for containing cathinone- and/or cathine-related alkaloids.     

Suppression of Regeneration in New Zealand Mountain Beech Forests is Dependent on Species of Introduced Deer

We compared the impacts on forest regeneration of introduced sika (Cervus nippon) and red (Cervus elaphus) deer in New Zealand. Plot data were used to compare mountain beech (Nothofagus solandri var. cliffortioides) regeneration between a region with sika deer, and four regions without sika deer. All regions surveyed had red deer present. In the region where sika deer had been present for more than a decade, there was evidence of poor mountain beech seedling regeneration. In the four regions without sika deer, there was evidence of a strong regenerative response at stands with low occupancy by trees. When compared to larger deer species, sika deer have a digestive morphology allowing greater dietary versatility, which may result in them impeding forest regeneration where red deer do not. In contrast to mountain beech, some small-leaved shrub species may have been competitively advantaged by intensive browsing from sika deer. This is contra to a current view that small-leaved shrub species with interlacing branches were able to tolerate browsing from extinct ratite birds, but not introduced deer. Sika deer have been introduced into countries where other deer species are indigenous, such as Canada, Denmark, Great Britain, Czech Republic, Ireland and the United States of America. Because of their dietary advantage, sika deer may have a greater potential to impede forest regeneration and competitively exclude larger deer species, particularly at low basal area sites where impacts on tree regeneration are likely to be greatest.     

Molecular phylogeny, diversification and character evolution in Lupinus (Fabaceae) with special attention to Mediterranean and African lupines

Phylogenetic relationships within the complex genus Lupinus are estimated from internal transcribed spacer (ITS) sequences of the nuclear ribosomal DNA repeat. The molecular data supports Lupinus as a distinct monophyletic group within the tribe Genisteae. Different geographical lineages are revealed within Lupinus, which are each restricted to either the Old or the New World. In the New World, the ITS data support an eastern-western geographic disjunction of the lupines and the recognition of some well-supported clades. In the Old World, almost all the previously recognized taxa are taxonomically well differentiated. The homogeneous African rough-seeded lupines, Scabrispermae, are strongly supported as a monophyletic group, which is distinct from the diverse and heterogeneous circum-Mediterranean smooth-seeded ones. The latter appear to have evolved as two lineages, in which are revealed some intersectional relationships. Also ITS data allow the assessment of the phylogenetic position of the newly discovered species, L. anatolicus (in the Old World) and L. jaimehintoniana (the Mexican tree lupin). The ITS phylogeny suggests a rapid initial radiation of the lupines subsequent to their divergence from a common ancestor. Moreover, the results indicate that the annual and perennial habits have evolved many times in Lupinus and suggest a role for generation time in affecting the evolutionary history of lupines. Data on adaptive processes and character evolution are re-examined and discussed in the light of the ITS phylogeny.These studies were supported by the research unit UMR-CNRS 6553 Ecobio – University of Rennes (France), and by the NSERC of Canada (grant to R.J. Bayer, at the University of Alberta). They are greatfully acknowledged. All the persons that have contributed in different ways to this work on Lupinus, summarized in this presentation, are greatly thanked. Particularly, we would like to mention Malika Aïnouche, Roland Greinwald, André Huon, W.K. Swiecicki, Billie L. Turner and Ludger Witte for their contributions.     

Examining monophyly in a large radiation of Madagascan butterflies (Lepidoptera: Satyrinae: Mycalesina) based on mitochondrial DNA data

The satyrine butterfly subtribe Mycalesina has undergone one of the more spectacular evolutionary radiations of butterflies in the Old World tropics. Perhaps the most phenotypically pronounced diversification of the group has occurred in the Malagasy region, where 68 currently recognized species are divided among five genera. Here, we report the results of phylogenetic analyses of sequence data from the cytochrome c oxidase II and cytochrome b mitochondrial genes, for a total of 54 mycalesine taxa, mostly from Madagascar. These molecular data complement an existing data set based on male morphological characters. The molecular results support the suggestion from morphology that three of the five Malagasy genera are paraphyletic and support the monophyly of at least three major morphological clades. Novel hypotheses of terminal taxon pairs are generated by the molecular data. Dense taxon sampling appears to be crucial for elucidating phylogenetic relationships within this large radiation. A potentially complex scenario for the origin of Malagasy mycalesines is proposed.     

A mobile element based phylogeny of Old World monkeys

SINEs (Short INterspersed Elements) are a class of non-autonomous mobile elements that are <500 bp in length and have no open reading frames. Individual SINE elements are essentially homoplasy free with known ancestral states, making them useful genetic systems for phylogenetic studies. Alu elements are the most successful SINE in primate genomes and have been utilized for resolving primate phylogenetic relationships and human population genetics. However, no Alu based phylogenetic analysis has yet been performed to resolve relationships among Old World monkeys. Using both a computational approach and polymerase chain reaction display methodology, we identified 285 new Alu insertions from sixteen Old World monkey taxa that were informative at various levels of catarrhine phylogeny. We have utilized these elements along with 12 previously reported loci to construct a phylogenetic tree of the selected taxa. Relationships among all major clades are in general agreement with other molecular and morphological data sets but have stronger statistical support.     

A complete generic phylogeny of Malpighiaceae inferred from nucleotide sequence data and morphology

? Premise of the study: The Malpighiaceae include ～1300 tropical flowering plant species in which generic definitions and intergeneric relationships have long been problematic. The goals of our study were to resolve relationships among the 11 generic segregates from the New World genus Mascagnia, test the monophyly of the largest remaining Malpighiaceae genera, and clarify the placement of Old World Malpighiaceae. ? Methods: We combined DNA sequence data for four genes (plastid ndhF, matK, and rbcL and nuclear PHYC) from 338 ingroup accessions that represented all 77 currently recognized genera with morphological data from 144 ingroup species to produce a complete generic phylogeny of the family. ? Key results and conclusions: The genera are distributed among 14 mostly well-supported clades. The interrelationships of these major subclades have strong support, except for the clade comprising the wing-fruited genera (i.e., the malpighioid+Amorimia, Ectopopterys, hiraeoid, stigmaphylloid, and tetrapteroid clades). These results resolve numerous systematic problems, while others have emerged and constitute opportunities for future study. Malpighiaceae migrated from the New to Old World nine times, with two of those migrants being very recent arrivals from the New World. The seven other Old World clades dispersed much earlier, likely during the Tertiary. Comparison of floral morphology in Old World Malpighiaceae with their closest New World relatives suggests that morphological stasis in the New World likely results from selection by neotropical oil-bee pollinators and that the morphological diversity found in Old World flowers has evolved following their release from selection by those bees.     

Generic delimitation and phylogenetic relationships within the subtribe Chironiinae (Chironieae: Gentianaceae), with special reference to Centaurium: evidence from nrDNA and cpDNA sequences

To better understand the evolutionary history of the genus Centaurium and its relationship to other genera of the subtribe Chironiinae (Gentianaceae: Chironieae), molecular analyses were performed using 80 nuclear ribosomal ITS and 76 chloroplast trnLF (both the trnL UAA intron and the trnL-F spacer) sequences. In addition, morphological, palynological, and phytochemical characters were included to a combined data matrix to detect possible non-molecular synapomorphies. Phylogenetic reconstructions support the monophyly of the Chironiinae and an age estimate of ca. 22 million years for the subtribe. Conversely, both molecular data sets reveal a polyphyletic Centaurium, with four well-supported main clades hereafter treated as separate genera. The primarily Mediterranean Centaurium s.s. is closely related to southern African endemics Chironia and Orphium, and to the Chilean species Centaurium cachanlahuen. The resurrected Mexican and Central American genus Gyrandra is closely related to Sabatia (from eastern North America). Lastly, the monospecific genus Exaculum (Mediterranean) forms a monophyletic group together with the two new genera: Schenkia (Mediterranean and Australian species) and Zeltnera (all other indigenous American centauries). Several biogeographical patterns can be inferred for this group, supporting a Mediterranean origin followed by dispersals to (1) North America, Central America, and South America, (2) southern Africa (including the Cape region), and (3) Australia and Pacific Islands.