Joseph A. Cook

Phylogeography of a post‐glacial colonizer: Microtus longicaudus (Rodentia: Muridae)

The molecular phylogeography of Microtus longicaudus was investigated with DNA sequences of the mitochondrial cytochrome b gene. We used phylogenetic and pairwise distance methods to reconstruct the history of the species with particular emphasis on the Pacific Northwest. Genetic variation across the species was consistent with vicariant events during the Pleistocene and subsequent northern postglacial expansion following the receding Laurentide and Cordilleran ice sheets. The largest break (> 6% uncorrected sequence divergence) was found to exist between populations found southeast of the Colorado River (eastern Arizona, Colorado, Wyoming and New Mexico) and all other western populations. Other well‐supported subclades were composed of samples from: (i) the islands and north coast of southeast Alaska; (ii) eastern Alaska, British Columbia, Washington and Oregon; and (iii) northern California, Idaho and Montana. Within subclades, divergence was low. Our results suggest that the close relationships among haplotypes within northern subclades are a result of recent colonization, whereas higher among‐subclade divergence is caused by genetic differentiation during prolonged periods of isolation, possibly as a result of mid‐Pleistocene climatic events.

MOLECULAR SYSTEMATICS OF A HOLARCTIC RODENT (MICROTUS: MURIDAE)

Abstract The Bering Land Bridge was the intermittent connection that allowed exchange of mammals between Asia and North America. Because some mammalian genera are widely distributed on both continents, recovery of phylogenetic histories of species within these genera may help reconstruct the sequence of intercontinental exchanges. We tested phylogenetic and biogeographic hypotheses in the widespread genus Microtus through parsimony and likelihood analysis of mtDNA-sequence data. The extant species of Microtus in North America are thought to be derived from multiple invasions from Asia or, alternatively, as a single invasion followed by autochthonous speciation. Mitochondrial cytochrome-b gene sequences were obtained for 78 individuals representing 24 species of Microtus. Data supported 1 clade of taiga voles (M. pennsylvanicus, M. montanus, M. townsendii, and M. canicaudus), a clade of Asian species (M. kikuchii, M. fortis, M. montebelli, and M. middendorffi), plus the Holarctic M. oeconomus and several other previously identified clades. M. gregalis also was found to be distant from M. abbreviatus and M. miurus, thus contradicting monophyly of the subgenus Stenocranius. Monophyly of North American species was supported, albeit weakly. Basal relationships were not robust, reflecting a single pulse of diversification about 1.3 × 106 years ago. This pulse mirrors the fossil record and may be partially responsible for the unstable taxonomic history.

Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): insight into deep and shallow history in northwestern North America

Phylogenetic relationships among the dusky shrew (Sorexmonticolus) and eight related species (S. bairdi, S. bendirii, S. neomexicanus, S.ornatus, S. pacificus, S. palustris, S. sonomae and S.vagrans) were assessed using sequences from the mitochondrial cytochrome b gene (801 bp). Analyses using parsimony and maximum likelihood revealed significant molecular variation not reflected in previous morphological studies of these species. Conversely, three morphologically defined species (S.bairdi, S.neomexicanusandS.pacificus) were poorly differentiated. SorexornatusandS.vagrans represented basal taxa for a more inclusive group that included: (i) a widespread Continental clade containing S.monticolus (Arizona to Alaska, including S. neomexicanus); (ii) a Coastal clade containing S.monticolus (Oregon to south‐east Alaska, including S. bairdiandS. pacificus); (iii) the semiaquatic species (S. bendiriiandS. palustris); and (iv) S.sonomae. Additional subdivision was observed within the Continental clade corresponding to populations from the northern and southern Rocky Mountains. Average uncorrected sequence divergence between the Coastal and Continental clades was 5.3% (range 4.5–6.2%), which exceeds many interspecific comparisons within this species complex and within the genus Sorex. Lack of resolution of internal nodes within topologies suggests a deep history of rapid diversification within this group. Late Pleistocene/Holocene glacial perturbations are reflected in the shallow phylogeographic structure within these clades in western North America. Our results suggest also that S. monticolus is not monophyletic under current taxonomic nomenclature. This perspective on phylogeographic history was developed within a growing comparative framework for other organisms in western North America.

A phylogeographic perspective on endemism in the Alexander Archipelago of southeast Alaska

Conservation plans for the North Pacific Coast are beginning to acknowledge that the old-growth forests remaining on the extensive archipelagos of the region may require a new management paradigm. Extensive timber harvesting activities on these islands may impact wildlife populations and be particularly detrimental to the large number of endemics. Because insular biotas have suffered a disproportionate number of documented extinctions worldwide, the documentation of taxonomic validity and spatial distribution of endemics should be a priority for management efforts. To date, few North Pacific coastal endemics have been reevaluated since their original descriptions. This study provides an independent view of endemism in the Alexander Archipelago of southeast Alaska through a phylogeographic assessment of eight species of mammals (Sorex monticolus, Glaucomys sabrinus, Microtus longicaudus, Clethrionomys rutilus, Clethrionomys gapperi, Martes americana, Mustela erminea, Ursus americanus). The molecular data (mitochondrial sequence variation of the cytochrome b gene) suggest a dynamic history of faunal interchange in the region. While some purported endemics show minimal levels of genetic divergence from other conspecific populations, other taxa appear to be more divergent than recognized by current taxonomy. Some species in the region are comprised of multiple clades or evolutionarily significant units. These reciprocally monophyletic lineages may be the result of multiple Holocene invasions (neoendemics) or they may have persisted in refugia (paleoendemics) in the region during Pleistocene glacial advances. This emerging historical perspective should have direct implications for the management of these endemic taxa.

Post‐glacial colonization of northwestern North America by the forest‐associated American marten (Martes americana, Mammalia: Carnivora: Mustelidae)

Phylogeographic patterns were used to assess intraspecific diversification of American martens (Martes americana). Within martens, two morphological groups (americana and caurina) have been recognized, though the level of distinction between them has been debated. We examined mitochondrial cytochrome b gene haplotypes from 680 martens to explore the colonization history of the Pacific Northwest and found two clades that correspond to the morphological groups. The widespread americana clade extends from interior Alaska south to Montana and eastward to Newfoundland and New England (i.e. northwestern, north‐central and northeastern North America). The caurina clade occurs in western North America, minimally extending from Admiralty Island (southeastern Alaska) south to Oregon and Wyoming. Our data indicated two colonization events for the Pacific Northwest (one by members of each clade) and were consistent with the persistence of populations throughout past glacial periods in eastern and western refugia. Due to vegetational and geological history following the past deglaciation, we hypothesize that martens of the caurina clade spread along the North Pacific Coast, and into southeastern Alaska, earlier than martens of the americana clade. Mismatch distributions for the americana clade were indicative of populations that recently experienced demographic expansion, while mismatch distributions for the caurina clade suggested that populations were at equilibrium. These clades are reciprocally monophyletic and distinctive (interclade divergence ranged from 2.5 to 3.0% (uncorrected p), whereas, intraclade divergence was < 0.7%), and two regions of sympatry have been identified. Genetic signatures of past admixture in hybrid zones may have been extinguished during subsequent glacial periods when ranges contracted. This recurrent pattern of relatively restricted western, or Pacific coastal, lineages and more widespread eastern, or interior continental, lineages exists across broad taxonomic groups and suggests a shared biogeographical history.

Should endemism be a focus of conservation efforts along the North Pacific Coast of North America

Abstract Most documented extinctions of vertebrates in the last 400 years have been island endemics. In this paper, we focus on the need to develop a historical framework to establish conservation priorities for insular faunas and, in particular, to test the validity of nominal endemics. We use the example of the islands of the North Pacific Coast (NPC) of North America, a region that includes approximately one-half of all mammals endemic to North American islands north of Mexico (seven species and 67 subspecies). Few of these endemics have been re-evaluated since their original descriptions, although many of these islands have been heavily impacted by habitat conversion, species introductions, over-exploitation, and secondary ripple effects. Evidence from molecular genetics and paleontology suggests that many taxa arrived in the region since the last glacial advance. Some of these nominal endemics show minimal differentiation, while others comprise multiple evolutionary lineages. The NPC may also have played an important role in the in situ diversification of some taxa (paleoendemics) during the Pleistocene. Evidence, such as new fossil discoveries and numerous described endemics, lends support for refugia hypotheses. However, these ideas cannot be tested until a better understanding of geographic variation and the evolutionary relationships of the fauna and flora of the North Pacific Coast is developed. This framework would provide significant insight into the dynamic biogeographic history of the region and help prioritize conservation efforts.

Molecular evolution of Holarctic martens (genus Martes, Mammalia: Carnivora: Mustelidae)

The Bering Land Bridge has served as a major corridor of interchange between the northern continents for many organisms. We investigated the phylogeny of all extant species of Martes (except for Martes gwatkinsi from India) to infer evolutionary relationships and characterize the extent of trans-Beringian movements. Analyses of complete sequences of the mitochondrial cytochrome b gene and partial sequences of the nuclear aldolase C gene (241bp) suggested that the genus Martes may be paraphyletic with respect to Gulo gulo. These data supported the fossil records indication that early radiations gave rise to two subgenera (Pekania and Charronia) and that a more recent, possibly rapid, radiation gave rise to species of the third subgenus (Martes). Two colonizations of North America are evident, one by members of the subgenus Pekania and another by member of the subgenus Martes. Contrary to hypotheses based on morphological evidence, the americana and caurina subspecies groups of Martes americana are not the result of independent colonizations of North America. The phylogenetic analyses of cytochrome b data were consistent with the recognition of these subspecies groups as monophyletic clades; however, variation in the aldolase C sequences indicated that these generally parapatric groups may interbreed in a region of limited geographic overlap.

Phylogenetic Diversification within the Sorex cinereus Group (Soricidae)

Abstract Phylogenetic relationships among 8 members of the Sorex cinereus group (S. camtschatica, S. cinereus, S. haydeni, S. jacksoni, S. portenkoi, S. preblei, S. pribilofensis, and S. ugyunak) and S. longirostris were estimated using DNA sequence data from 2 mitochondrial genes, cytochrome b (1,140 base pairs) and nicotinamide adenine dinucleotide dehydrogenase 4 (582 base pairs). S. hoyi, S. monticolus, S. palustris, S. tenellus, S. trowbridgii, and S. vagrans also were included in our analyses. Phylogenetic analyses of the combined data recovered 2 major clades within the species group: a northern clade that includes the Beringian species (S. camtschatica, S. jacksoni, S. portenkoi, S. pribilofensis, and S. ugyunak), S. haydeni, and S. preblei and a southern clade that includes S. cinereus and S. longirostris. Mitochondrial DNA clades generally corresponded to previously identified morphological groups with 2 exceptions: inclusion of S. longirostris with S. cinereus in the southern clade and inclusion of S. preblei within the northern clade. With the exception of the 5 Beringian species, taxa were readily differentiated with strong bootstrap support in our topologies. We also noted phylogenetic concordance with the general ecological affiliations of each species; the northern clade generally includes xeric-affiliated species, whereas the southern clade includes species with mesic habitat affinities.

Molecular Phylogeny of Tuco-Tucos, Genus Ctenomys (Rodentia: Octodontidae): Evaluation of the mendocinus Species Group and the Evolution of Asymmetric Sperm

The phylogenetic relationships among 23 individuals representing 14 species of underground hystricognath rodents of the genus Ctenomys were studied by analyzing variation of complete cytochrome b gene sequences. Maximum parsimony, neighbor joining, and maximum likelihood analyses were performed, using the octodontine genera Octodon and Tympanoctomys as outgroups. Our analyses support previous studies based on chromosomes and skull morphology that suggested a clade comprised of Argentinean and Uruguayan populations of C. rionegrensis. This clade is closely related to one comprised of C. flamarioni and the C. mendocinus species complex. Our analyses provide evidence that the symmetric sperm morph, which is common to other South American hystricognath rodents, is the plesiomorphic character state in Ctenomys and in Hystricognathi. Our analyses do not support the hypothesis that the sperm morphs define two major lineages of tuco-tuco species, because species with asymmetric sperm are diphyletic on the basis of cytochrome b sequences, and this morphology appears to have evolved twice in Ctenomys.

Phylogenetic analysis of northern hair seals based on nucleotide sequences of the mitochondrial cytochrome b gene

Phylogenetic analysis was performed on a 458-base pair sequence from the mitochondrial cytochrome b gene of northern hair seals (Phocidae: Phocinae) including Phoca hispida, Phoca largha, Phoca vitulina, Phoca fasciata, Phoca groenlandica, Halichoerus grypus, Cystophora cristata , and Erignathus barbatus . Results suggest revision of currently accepted phylogenetic relationships among the Phocinae. Both neighbor-joining and parsimony analyses indicate a sister-taxon relationship between the gray seal, H. grypus , and the ringed seal, P. hispida .