Historical Biogeographic Events Research Articles

Seascape Genetics and Distinct Intraspecific Diversification of the Decapod Nephrops norvegicus in the Adriatic Sea.

Norway lobster Nephrops norvegicus, a prized decapod crustacean species, is found at different depths across the East Atlantic Ocean and Mediterranean Sea. Despite management efforts, the stocks are globally characterised as overexploited. In the present study, the impact of biogeographical boundaries on the phylogeographical and demographic population status was investigated within the Adriatic Sea, addressing important genetic indices for decapod functional conservation management. Central Mediterranean, Adriatic Sea A total of 482 individuals of Nephrops divided into the 12 samples were collected across biogeographical range of the Adriatic Sea. Using the mtDNA D-loop and microsatellite markers, methods of phylogeography and seascape genetics were applied to infer offshore versus coastal population divergence, demography and structure. Significant findings include genetic differentiation between offshore and coastal samples, with higher diversity indices in open waters. The limited gene flow observed between these two areas emphasises the self-sustained nature of coastal populations. Recent demographic changes in coastal populations reflect geographical constraints, fishing pressures and fluctuations in self-recruitment success. Additionally, the study reveals historical biogeographic events shaping the Adriatic populations, with evidence suggesting lineage divergence during the upper Pleistocene and postglacial recolonisation from southern Adriatic refugia. The role of biogeographical conditions in shaping genetic structure and limited gene flow between inshore and offshore areas underscore the need for improved management strategies, emphasising the importance of marine protected areas in conserving coastal populations and maintaining overall genetic diversity of the Norway lobster in the Adriatic Sea. Genomic monitoring within current management practices is recommended.

Geological Heritage, Biodiversity and Culture Linkage in Raja Ampat Geopark: An Introduction

Raja Ampat became globally known since researeh results revealed the magnificence of its marine biodiversity that was incomparable, and became the best tourism diving destination. As part of the Geopark, understanding of science and knowledge from various fields has been gradually revealed and curated in Raja Ampat. This article will be an introduction to the disclosure of the relationship between geological heritage, biodiversity, and culture in the Raja Ampat Geopark, synthesized through literature studies, interviews and ground checks conducted by various parties. As a result, at least three relations was explained, i.e. (1) the historical biogeographic events of Raja Ampat determined the form of thirteen terrestrial ecosystems and the present of endemic species; (2) the geological heritage of dolines and lagoons creates unique ecosystems for certain marine species; (3) also inter-connectivity between nature and the cultural values passed down by Raja Ampat's ancestors that documented in various forms, like wisdom, folklore and art rocks. In conclusion, we also identified challenges and future directions regarding this emerging field, of which has been adapted into ecotourism implementation within Geopark Raja Ampat.

Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae)

Characinae is one of the most species-rich subfamilies of Characidae and holds special taxonomic importance because it includes Charax, type-genus of Characidae and Characiformes. Currently, the monophyly and the hypotheses of intergeneric and interspecific relationships of Characinae are based on a few morphological and molecular studies but all with low species coverage. Given their diversity, taxonomic importance, and the lack of a taxon-dense phylogeny, we sought to buttress the systematic understanding of Characinae collecting DNA sequence data from ultraconserved elements (UCEs) of the genome from 98 specimens covering 57 species (61%) plus 17 characiforms as outgroups. We used maximum likelihood, Bayesian inference, and coalescent-based species tree approaches and the resulting phylogeny with 1,300 UCE loci (586,785 characters) reinforced the monophyly of the subfamily as well as of six genera: Acestrocephalus, Charax, Cynopotamus, Galeocharax, Phenacogaster, and Roeboides. The phylogeny provides a hypothesis of intergeneric and interspecific relationships for the subfamily with Phenacogaster sister to all genera, and Acanthocharax sister to Cynopotamini (Cynopotamus (Acestrocephalus Galeocharax)) and Characini (Charax Roeboides). We propose a new tribe Acanthocharacini to allocate Acanthocharax, two subclades for Phenacogaster, two for Cynopotamus, three for Charax, and reinforced the four subclades for Roeboides previously identified by morphological studies. Additionally, we generated a time-calibrated phylogeny for Characinae that suggested an initial diversification during the Miocene at around 19 million years ago and discussed historical biogeographic events for major subclades. The results obtained here will contribute to the development of further research on the evolutionary processes modulating species diversification in Characinae.

Deep‐sea squat lobster biogeography (Munidopsidae: Leiogalathea) unveils Tethyan vicariance and evolutionary patterns shared by shallow‐water relatives

AbstractThe ecology, abundance and diversity of galatheoid squat lobsters make them an ideal group to study deep‐sea diversification processes. Here, we reconstructed the evolutionary and biogeographic history of Leiogalathea, a genus of circum‐tropical deep‐sea squat lobsters, in order to compare patterns and processes that have affected shallow‐water and deep‐sea squat lobster species. We first built a multilocus phylogeny and a calibrated species tree with a relaxed clock using StarBEAST2 to reconstruct evolutionary relationships and divergence times among Leiogalathea species. We used BioGeoBEARS and a DEC model, implemented in RevBayes, to reconstruct ancestral distribution ranges and the biogeographic history of the genus. Our results showed that Leiogalathea is monophyletic and comprises four main lineages; morphological homogeneity is common within and between clades, except in one; the reconstructed ancestral range of the genus is in the Atlantic and Indian oceans (Tethys). They also revealed the divergence of the Atlantic species around 25 million years ago (Ma), intense cladogenesis 15–25 Ma and low levels of speciation over the last 5 million years (Myr). The four Leiogalathea lineages showed similar patterns of speciation: allopatric speciation followed by range expansion and subsequent stasis. Leiogalathea started diversifying during the Oligocene, likely in the Tethyan. The Atlantic lineage then split from its Indo‐Pacific sister group due to vicariance driven by closure of the Tethys Seaway. The Atlantic lineage is less speciose compared with the Indo‐Pacific lineages, with the Tropical Southwestern Pacific being the current centre of diversity. Leiogalathea diversification coincided with cladogenetic peaks in shallow‐water genera, indicating that historical biogeographic events similarly shaped the diversification and distribution of both deep‐sea and shallow‐water squat lobsters.

Estimation of Evolutionary Rates of Mitochondrial DNA in Two Japanese Wood Mouse Species Based on Calibrations with Quaternary Environmental Changes.

Reliable estimates of evolutionary rates of mitochondrial DNA might allow us to build realistic evolutionary scenarios covering broad time scales based on phylogenetic inferences. In the present study, we sought to obtain estimates of evolutionary rates in murine rodents using calibrations against historical biogeographic events. We first assumed that land-bridge-like structures that appeared intermittently at glacial maxima with 100,000-year intervals shaped the divergence patterns of cytochrome b (Cytb) sequences (1140 bp) of the larger Japanese wood mouse Apodemus speciosus. The comparison of sequences from peripheral remote islands that are separated from one another by deep straits allowed us to estimate mitochondrial DNA evolutionary rates (substitutions/site/million years) to be 0.027 to 0.036, with presumed calibrations from 140,000, 250,000, 350,000, and 440,000 years ago. Second, we addressed rapid expansion events inferred from analyses of the Cytb sequences of the lesser Japanese wood mouse A. argenteus. We detected five expansion signals in the dataset and established three categories based on the expansion parameter tau values: 3.9, 5.6-5.7, and 7.8-8.1. Considering that the climate became warmer 15,000, 53,000, and 115,000 years ago after preceding periods of rapid cooling, we calculated evolutionary rates to be 0.114, 0.047, and 0.031, respectively. This preliminary concept of the evolutionary rates on a time scale from 15,000 to 440,000 years ago for the wood mouse should be refined and tested in other species of murine rodents, including mice and rats.

Evolutionary History of the Asian Horned Frogs (Megophryinae): Integrative Approaches to Timetree Dating in the Absence of a Fossil Record.

Molecular dating studies typically need fossils to calibrate the analyses. Unfortunately, the fossil record is extremely poor or presently nonexistent for many species groups, rendering such dating analysis difficult. One such group is the Asian horned frogs (Megophryinae). Sampling all generic nomina, we combined a novel ∼5 kb dataset composed of four nuclear and three mitochondrial gene fragments to produce a robust phylogeny, with an extensive external morphological study to produce a working taxonomy for the group. Expanding the molecular dataset to include out-groups of fossil-represented ancestral anuran families, we compared the priorless RelTime dating method with the widely used prior-based Bayesian timetree method, MCMCtree, utilizing a novel combination of fossil priors for anuran phylogenetic dating. The phylogeny was then subjected to ancestral phylogeographic analyses, and dating estimates were compared with likely biogeographic vicariant events. Phylogenetic analyses demonstrated that previously proposed systematic hypotheses were incorrect due to the paraphyly of genera. Molecular phylogenetic, morphological, and timetree results support the recognition of Megophryinae as a single genus, Megophrys, with a subgenus level classification. Timetree results using RelTime better corresponded with the known fossil record for the out-group anuran tree. For the priorless in-group, it also outperformed MCMCtree when node date estimates were compared with likely influential historical biogeographic events, providing novel insights into the evolutionary history of this pan-Asian anuran group. Given a relatively small molecular dataset, and limited prior knowledge, this study demonstrates that the computationally rapid RelTime dating tool may outperform more popular and complex prior reliant timetree methodologies.

A review of the Pseudocleonus subgenus Phryganocleonus Arnol’di, with the description of a new species from Afghanistan (Coleoptera, Curculionidae: Lixinae)

Pseudocleonus (Phryganocleonus) kratkyi sp. n. is described from Afghanistan. Some remarks on the taxonomy of the subgenus Phryganocleonus are given, with a key to the species. Lectotypes of Pseudocleonus guldarensis Arnol’di, Ps. iskanderi Arnol’di, and Ps. tadzhika Arnol’di are designated. Hypotheses on the historical biogeographical events that may have caused species differentiation are proposed.

Historical biogeography resolves the origins of endemic Arabian toad lineages (Anura: Bufonidae): Evidence for ancient vicariance and dispersal events with the Horn of Africa and South Asia.

BackgroundThe Arabian Peninsula is home to a unique fauna that has assembled and evolved throughout the course of major geophysical events, including the separation of the Arabian Plate from Africa and subsequent collision with Eurasia. Opportunities for faunal exchanges with particular continents occurred in temporally distinct periods, and the presence of African, Western Eurasian, and South Asian derived taxa on the Arabian Peninsula signifies the complexity of these historical biogeographic events. The six true toad species (family Bufonidae) endemic to the Arabian Peninsula present a considerable taxonomic and biogeographic challenge because they are part of a global bufonid radiation, including several genera surrounding the Arabian Peninsula, and difficult to discriminate morphologically. As they could be derived from African, Western Eurasian, or South Asian toad groups, elucidating their evolutionary relationships has important implications for historical biogeography. Here, we analyze a global molecular data set of 243 bufonid lineages, with an emphasis on new sampling from the Horn of Africa, Western Eurasia, South Asia, and the Arabian Peninsula, to reconstruct the evolutionary relationships of the Arabian species. We produce a robust time-calibrated phylogeny to infer the biogeographic history of this group on and around the Arabian Peninsula.ResultsOur phylogenetic analyses indicate two of the endemic Arabian toad species, “Bufo” tihamicus and “Bufo” arabicus, evolved independently within the African genus Amietophrynus. We confirm the Arabian species Duttaphrynus dhufarensis is of South Asian origin, but do not find evidence for the Asian genus Duttaphrynus being present in the Horn of Africa, discrediting a previously proposed Asian bufonid dispersal event to Africa. We also do not find evidence of the African genus Amietophrynus occurring in South Asia, suggesting that unlike many other vertebrate taxa, toads have not used the Arabian Peninsula as a stepping-stone for trans-continental dispersal. Our divergence dating estimates strongly suggest the formation of the Red Sea drove simultaneous divergences between two of the Arabian species (A. tihamicus comb. nov. and A. arabicus comb. nov.) and their closest mainland African relatives in the Early Miocene. We estimate the divergence of D. dhufarensis with its closest South Asian relatives occurred in the mid to Late Miocene, suggesting the temporary or permanent land connections between the Arabian plate and Eurasia facilitated dispersal of this lineage to the Arabian Peninsula.ConclusionsThe Arabian bufonid assemblage, despite being comparatively depauperate with respect to surrounding continents, exemplifies the faunal pattern of the Arabian Peninsula, namely being a complex admixture of African, Western Eurasian, and South Asian elements. The historical biogeographic patterns exhibited by Arabian toads and their allies are concordant with studies of other vertebrate taxa, building support for the role of major geological events in driving simultaneous vicariance and dispersal events around the Arabian Peninsula. Although many taxa or groups exhibiting disjunct Afro-Arabian distributions appear to have dispersed more recently from the Horn of Africa via a southern land bridge or overwater dispersal, both Amietophrynus tihamicus and A. arabicus likely represent true African relicts resulting from vicariance associated with the Red Sea formation, a pattern that so far is rare among the vertebrate species investigated.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0417-y) contains supplementary material, which is available to authorized users.

Elevation and moths in a central eastern Queensland rainforest

Elevational gradients are powerful natural experiments for the investigation of ecological responses to changing climates. Automated modified Pennsylvania light traps were used to sample macro-moth assemblages for three consecutive nights at each of 24 sites ranging from 200 m asl to 1200 m asl within continuous tropical rainforest at Eungella, Queensland, Australia (21°S, 148°E). A total of 13 861 individual moths representing approximately 713 morphospecies and 10 045 individuals belonging to approximately 607 morphospecies where sampled during November 2013 and March 2014 respectively. Moth assemblages exhibited a strong elevational signal during both sampling seasons; we grouped these into lowland and upland assemblages. The dispersal pattern of moth assemblages across the landscape reflected the stratification of vegetation communities across elevation and correlated with shifts in eco-physical variables, most notably temperature and substrate organic matter. Regional historical biogeographical events likely contributed to the observed patterns. The analysis presented here identifies a set of statistically defined elevationally restricted moths which may be of use as part of a multi-taxon predictor set for monitoring future ecosystem level changes associated with elevation and, by implication, with climate.

Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography.

Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analysed 10 microsatellite loci from over 1900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses, we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles, and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation and management.

Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)?

Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, have become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multilocus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure moulded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ('refugia within refugia') and emphasize the importance of the Balkans as a major European biodiversity centre. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies.

Inferring geographic range evolution of a pantropical tribe in the coffee family (Lasiantheae, Rubiaceae) in the face of topological uncertainty

In this study we explore what historical biogeographic events are responsible for the wide and disjunct distribution of extant species in Lasiantheae, a pantropical group of trees and shrubs in the coffee family. Three of the genera in the group, Lasianthus, Saldinia, and Trichostachys, are found to be monophyletic, while there are indications that the fourth, Ronabea, is paraphyletic. We also address how the uncertainty in topology and divergence times affects the level of confidence in the biogeographic reconstruction. A data set consisting of chloroplast and nuclear ribosomal DNA data was analyzed using a Bayesian relaxed molecular clock approach to estimate phylogenetic relationships and divergence times, and the dispersal–extinction–cladogenesis (DEC) method to reconstruct geographic range evolution. Our results show that the Lasiantheae stem lineage originated in the neotropics, and the group expanded its range to the palaeotropics during the Eocene, either by continental migration through the boreotropics or by transatlantic long-distance dispersal. Two cases of Oligocene/Miocene over water-dispersal were also inferred, once from the paleotropics to the neotropics within Lasianthus, and once to Madagascar, concurrent with the origin of Saldinia. A lot of the diversification within Lasianthus took place during the Miocene and may have been influenced by climatic factors such as a period of markedly warm and moist climate in Asia and the aridification of the interior of the African continent. When biogeographic reconstructions were averaged over a random sample of 1000 dated phylogenies, the confidence in the biogeographic reconstruction decreased for most nodes, compared to when a single topology was used. A good understanding of phylogenetic relationships is necessary to understand the biogeographic history of a group, bit since the phylogeny is rarely completely known it is important to include phylogenetic uncertainty in biogeographic analysis. For nodes where the resolution is uncertain, the use of a single “best” topology as a basis for biogeographic analysis will result in inflated confidence in a biogeographic reconstruction which may be just one of several possible reconstructions.

Inferring the biogeographic origins of inter‐continental disjunct endemics using a Bayes‐DIVA approach

AbstractThe arcto‐Tertiary relictual flora is comprised of many genera that occur non‐contiguously in the temperate zones of eastern Asia, Europe, eastern North America, and western North America. Within each distributional area, species are typically endemic and may thus be widely separated from closely related species within the other areas. It is widely accepted that this common pattern of distribution resulted from of the fragmentation of a once more‐continuous arcto‐Tertiary forest. The historical biogeographic events leading to the present‐day disjunction have often been investigated using a phylogenetic approach. Limitations to these previous studies have included phylogenetic uncertainty and uncertainty in ancestral range reconstructions. However, the recently described Bayes‐DIVA method handles both types of uncertainty. Thus, we used Bayes‐DIVA analysis to reconstruct the stem lineage distributions for 185 endemic lineages from 23 disjunct genera representing 17 vascular plant families. In particular, we asked whether endemic lineages within each of the four distributional areas more often evolved from (1) widespread ancestors, (2) ancestors dispersed from other areas, or (3) endemic ancestors. We also considered which of these three biogeographic mechanisms may best explain the origins of arcto‐Tertiary disjunct endemics in the neotropics. Our results show that eastern Asian endemics more often evolved from endemic ancestors compared to endemics in Europe and eastern and western North America. Present‐day endemic lineages in the latter areas more often arose from widespread ancestors. Our results also provide anecdotal evidence for the importance of dispersal in the biogeographic origins of arcto‐Tertiary species endemic in the neotropics.

Species delimitation and phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae): cryptic diversity in North American tarantulas.

BackgroundThe primary objective of this study is to reconstruct the phylogeny of the hentzi species group and sister species in the North American tarantula genus, Aphonopelma, using a set of mitochondrial DNA markers that include the animal “barcoding gene”. An mtDNA genealogy is used to consider questions regarding species boundary delimitation and to evaluate timing of divergence to infer historical biogeographic events that played a role in shaping the present-day diversity and distribution. We aimed to identify potential refugial locations, directionality of range expansion, and test whether A. hentzi post-glacial expansion fit a predicted time frame.Methods and FindingsA Bayesian phylogenetic approach was used to analyze a 2051 base pair (bp) mtDNA data matrix comprising aligned fragments of the gene regions CO1 (1165 bp) and ND1-16S (886 bp). Multiple species delimitation techniques (DNA tree-based methods, a “barcode gap” using percent of pairwise sequence divergence (uncorrected p-distances), and the GMYC method) consistently recognized a number of divergent and genealogically exclusive groups.ConclusionsThe use of numerous species delimitation methods, in concert, provide an effective approach to dissecting species boundaries in this spider group; as well they seem to provide strong evidence for a number of nominal, previously undiscovered, and cryptic species. Our data also indicate that Pleistocene habitat fragmentation and subsequent range expansion events may have shaped contemporary phylogeographic patterns of Aphonopelma diversity in the southwestern United States, particularly for the A. hentzi species group. These findings indicate that future species delimitation approaches need to be analyzed in context of a number of factors, such as the sampling distribution, loci used, biogeographic history, breadth of morphological variation, ecological factors, and behavioral data, to make truly integrative decisions about what constitutes an evolutionary lineage recognized as a “species”.

Metacommunity phylogenetics: separating the roles of environmental filters and historical biogeography

Biogeographical, evolutionary and ecological processes interact to regulate patterns in metacommunities. However, as there are few quantitative methods for evaluating their joint effects, resolving this interaction is difficult. We develop a method that aims to evaluate the interaction between phylogenetic structure, historical biogeographic events and environmental filtering in driving species distributions in a large-scale metacommunity. Using freshwater zooplankton as a case study, we contrast the phylogenetic metacommunity structure of calanoid copepods and an ecologically similar but more vagile group, daphniids, in the northeastern US. We find that legacies of historical biogeographical events have strongly constrained calanoid distributions within this area, but that adaptation to different water chemistry and lake morphology drives the metacommunity structure of daphniids. Our findings show that biogeographic history and metacommunity processes jointly regulate community structure in these lakes and suggest that this also depends on factors that affect the colonization rate of different types of organisms.

The phylogeography of Indoplanorbis exustus (Gastropoda: Planorbidae) in Asia.

BackgroundThe freshwater snail Indoplanorbis exustus is found across India, Southeast Asia, central Asia (Afghanistan), Arabia and Africa. Indoplanorbis is of economic importance in that it is responsible for the transmission of several species of the genus Schistosoma which infect cattle and cause reduced livestock productivity. The snail is also of medical importance as a source of cercarial dermatitis among rural workers, particularly in India. In spite of its long history and wide geographical range, it is thought that Indoplanorbis includes only a single species. The aims of the present study were to date the radiation of Indoplanorbis across Asia so that the factors involved in its dispersal in the region could be tested, to reveal potential historical biogeographical events shaping the phylogeny of the snail, and to look for signs that I. exustus might be polyphyletic.ResultsThe results indicated a radiation beginning in the late Miocene with a divergence of an ancestral bulinine lineage into Assam and peninsular India clades. A Southeast Asian clade diverged from the peninsular India clade late-Pliocene; this clade then radiated at a much more rapid pace to colonize all of the sampled range of Indoplanorbis in the mid-Pleistocene.ConclusionsThe phylogenetic depth of divergences between the Indian clades and Southeast Asian clades, together with habitat and parasitological differences suggest that I. exustus may comprise more than one species. The timescale estimated for the radiation suggests that the dispersal to Arabia and to Southeast Asia was facilitated by palaeogeographical events and climate change, and did not require human involvement. Further samples from Afghanistan, Africa and western India are required to refine the phylogeographical hypothesis and to include the African Recent dispersal.

Phylogenetic structure of the Thomomys bottae–umbrinus complex in North America

The phylogeography of the Thomomys bottae–umbrinus complex in the United States and Mexico was assessed with sequences of the mitochondrial cytochrome b gene. These sequences were obtained from 225 individuals representing 108 locations over the range, including 56 sequences from GenBank. 110 (500 bp) sequences were used for Bayesian inference and neighbor-joining analyses, and 34 (1140 bp) specimens from the main clades obtained from the Bayesian inference were used in maximum-parsimony and maximum-likelihood analyses. The different analyses indicate significant variation within the species complex that averages 13% among major groups of genetic differences among Thomomys bottae–umbrinus. The overall pattern of geographic variation is not concordant with the current taxonomy. To the contrary, eight monophyletic groups are supported by all analyses and can be considered phylogenetic species. Overall divergence among these groups appears influenced by historical biogeographic events active during the Pliocene and Pleistocene.

Species status and phylogeography of two closely related Coptolabrus species (Coleoptera: Carabidae) in South Korea inferred from mitochondrial and nuclear gene sequences

We investigated the species status and intraspecific phylogeography in South Korea of two ground beetle species, Coptolabrus jankowskii and Coptolabrus smaragdinus (Coleoptera: Carabidae), using statistical parsimony networks and nested clade analyses based on sequences from the mitochondrial cytochrome oxidase subunit I (COI) and nuclear phosphoenolpyruvate carboxykinase (PepCK) and wingless (Wg) genes. Although traditional parsimony tree construction generally failed to resolve interspecific relationships and construct biologically meaningful genealogies, analysis using statistical parsimony networks yielded statistically significant inter- and intraspecific genealogical structures. We found that although these two species represent a notable case of trans-species polymorphisms in both mitochondrial and nuclear gene sequences, their status as separate species was evidenced by the nonrandom association between species and nested clades at various nesting levels. The exceptional occurrence of shared identical or very similar COI sequences was considered to be the result of introgressive hybridization. In addition, range expansion and fragmentation events across the Korean Peninsula and adjacent islands were inferred from nested clade phylogeographical analyses. The COI gene revealed the geographical divergence of major eastern and western clades and historical biogeographical events within each major clade, whereas the nuclear PepCK gene, which did not reveal corresponding east-west clades, indicated past fragmentation and range expansion across wide areas that may have been the result of older biogeographical events. Thus, phylogeographical inferences drawn from analyses of mitochondrial and nuclear genes can reveal different and potentially complementary information about phylogeographical processes.

White-Tailed Deer Restoration to the Southeastern United States: Evaluating Genetic Variation

Protective legislation and restocking were used to restore white-tailed deer (Odocoileus virginianus) to the southeastern United States (U.S.) following declines that occurred during the nineteenth century. Although stocking and protection of native herds are often key components of deer management programs, the degree to which these strategies contributed to recovery of southeastern white-tailed deer has not been determined. We used mitochondrial DNA (mtDNA) restriction-site variation and allozyme diversity to characterize gene flow patterns and genetic differentiation among white-tailed deer populations in the southeastern U.S. and evaluated the effectiveness of management programs for restoring white-tailed deer to the region. Compared with white-tailed deer in northern areas of North America, deer in the southeastern U.S. exhibited a high level of mtDNA subdivision (Gs, = 0.621) that may be attributable to site philopatry of females. Relative to mtDNA, the extent of allozyme differentiation (FsT = 0.153) indicated a bias in dispersal (gene flow) toward males (3:1), suggesting that managers should regulate the degree to which males are preferentially harvested to preserve the exchange of genetic information among populations. Geographic patterns of genetic variation in white-tailed deer were congruent with those in unrelated taxa, implicating the common influence of historical biogeographic events in shaping contemporary genetic structure. Similarities in geographic variation between white-tailed deer and other vertebrates inhabiting this region indicated that deer populations in the southeastern U.S. are descended from native herds and that relocated deer have contributed insignificantly to the genetic composition of extant populations. J. WILDL. MANAGE. 58(4):686-697

HISTORICAL BIOGEOGRAPHY AND CONTEMPORARY PATTERNS OF MITOCHONDRIAL DNA VARIATION IN WHITE-TAILED DEER FROM THE SOUTHEASTERN UNITED STATES.

Mitochondrial DNA (mtDNA) was used to characterize patterns of geographic variation among white-tailed deer (Odocoileus virginianus) populations in the southeastern United States. Fifteen restriction enzymes were employed to survey and map 99 restriction sites in 142 deer from 18 localities in five southeastern states. Phylogenetic analysis revealed three primary groups of haplotypes: (1) southern Florida and the Florida Keys, (2) the remainder of peninsular Florida northward to South Carolina, and (3) the Florida panhandle westward to Mississippi. Geographical heterogeneity in haplotype frequencies suggests that stochastic lineage sorting or isolation by distance are not important determinates of mtDNA differentiation among deer populations. The pattern of mtDNA variation in white-tailed deer is concordant spatially with those observed in unrelated taxa suggesting the common influence of historical biogeographic events. The data (1) support previous hypotheses that relate contemporary patterns of intraspecific phylogeography in northern Florida to the physiogeographic history of the region; and (2) suggest that genetic differentiation in southern Florida may be attributable to episodes of Pleistocene dispersal. Despite potentially high vagility and human intervention, ecological and demographic characteristics of deer have effectively preserved the historical pattern of intraspecific mtDNA differentiation.