GENETICS OF HOST-CACTUS RESPONSE AND LIFE-HISTORY EVOLUTION AMONG ANCESTRAL AND DERIVED POPULATIONS OF CACTOPHILIC DROSOPHILA MOJAVENSIS

The extent of host-specific genetic variation for two life-history traits, egg to adult developmental time and viability, and one morphological trait closely tied to fitness, adult thorax size, was exposed by employing a nested half-sib/full-sib breeding design with Baja and mainland populations of Drosophila mojavensis recently extracted from nature. This study was motivated by the presence of substantial variation in life histories among populations of D. mojavensis that use the fermenting tissues of particular species of columnar cacti for feeding and breeding in the Sonoran Desert. Full-sib progeny from all sire-dam crosses were split into cultures of agria cactus, Stenocereus gummosus, and organ pipe cactus, S. thurberi, to examine patterns of genotype-by-environment interaction for these fitness components. Baja flies expressed shorter egg-to-adult developmental times, higher viabilities, and smaller body sizes than mainland flies consistent with previous studies. Significant sire and dam components of variance were exposed for developmental time and thorax size. Genotype-by-environment interactions were significant at the level of dams for developmental time and nearly significant for viability (P = 0.09). Narrow- and broad-sense heritabilities were influenced by host cactus, sex, and population. No strong pattern of genetic correlation emerged among fitness components suggesting that host-range expansion has not been accompanied by formation of coadapted life histories, yet the ability to estimate genetic correlations and their standard errors was compromised by the unbalanced nature of the data set. Genetic correlations in performance across cacti were slightly positive, evidence for ecological generalism among populations explaining the observed pattern of multiple host cactus use within the species range of D. mojavensis.     

Does relaxed predation drive phenotypic divergence among insular populations?

The evolution of striking phenotypes on islands is a well‐known phenomenon, and there has been a long‐standing debate on the patterns of body size evolution on islands. The ecological causes driving divergence in insular populations are, however, poorly understood. Reduced predator fauna is expected to lower escape propensity, increase body size and relax selection for crypsis in small‐bodied, insular prey species. Here, we investigated whether escape behaviour, body size and dorsal coloration have diverged as predicted under predation release in spatially replicated islet and mainland populations of the lizard species Podarcis gaigeae. We show that islet lizards escape approaching observers at shorter distances and are larger than mainland lizards. Additionally, we found evidence for larger between‐population variation in body size among the islet populations than mainland populations. Moreover, islet populations are significantly more divergent in dorsal coloration and match their respective habitats poorer than mainland lizards. These results strongly suggest that predation release on islets has driven population divergence in phenotypic and behavioural traits and that selective release has affected both trait means and variances. Relaxed predation pressure is therefore likely to be one of the major ecological factors driving body size divergence on these islands.     

GENETICS OF INCIPIENT SPECIATION IN DROSOPHILA MOJAVENSIS. III. LIFE‐HISTORY DIVERGENCE IN ALLOPATRY AND REPRODUCTIVE ISOLATION

We carried out a three‐tiered genetic analysis of egg‐to‐adult development time and viability in ancestral and derived populations of cactophilic Drosophila mojavensis to test the hypothesis that evolution of these life‐history characters has shaped premating reproductive isolation in this species. First, a common garden experiment with 11 populations from Baja California and mainland Mexico and Arizona reared on two host species revealed significant host plant X region and population interactions for viability and development time, evidence for host plant adaptation. Second, replicated line crosses with flies reared on both hosts revealed autosomal, X chromosome, cytoplasmic, and autosome X cactus influences on development time. Viability differences were influenced by host plants, autosomal dominance, and X chromosomal effects. Many of the F₁, F₂, and backcross generations showed evidence of heterosis for viability. Third, a QTL analysis of male courtship song and epicuticular hydrocarbon variation based on 1688 Baja × mainland F₂ males also revealed eight QTL influencing development time differences. Mainland alleles at six of these loci were associated with longer development times, consistent with population‐level differences. Eight G × E interactions were also detected caused by longer development times of mainland alleles expressed on a mainland host with smaller differences among Baja genotypes reared on the Baja host plant. Four QTL influenced both development time and epicuticular hydrocarbon differences associated with courtship success, and there was a significant QTL‐based correlation between development time and cuticular hydrocarbon variation. Thus, the regional shifts in life histories that evolved once D. mojavensis invaded mainland Mexico from Baja California by shifting host plants were genetically correlated with variation in cuticular hydrocarbon‐based mate preferences.     

Body Size Evolution in Insular Speckled Rattlesnakes (Viperidae: Crotalus mitchellii)

Background

Speckled rattlesnakes (Crotalus mitchellii) inhabit multiple islands off the coast of Baja California, Mexico. Two of the 14 known insular populations have been recognized as subspecies based primarily on body size divergence from putative mainland ancestral populations; however, a survey of body size variation from other islands occupied by these snakes has not been previously reported. We examined body size variation between island and mainland speckled rattlesnakes, and the relationship between body size and various island physical variables among 12 island populations. We also examined relative head size among giant, dwarfed, and mainland speckled rattlesnakes to determine whether allometric differences conformed to predictions of gape size (and indirectly body size) evolving in response to shifts in prey size.

Methodology/Principal Findings

Insular speckled rattlesnakes show considerable variation in body size when compared to mainland source subspecies. In addition to previously known instances of gigantism on Ángel de la Guarda and dwarfism on El Muerto, various degrees of body size decrease have occurred frequently in this taxon, with dwarfed rattlesnakes occurring mostly on small, recently isolated, land-bridge islands. Regression models using the Akaike information criterion (AIC) showed that mean SVL of insular populations was most strongly correlated with island area, suggesting the influence of selection for different body size optima for islands of different size. Allometric differences in head size of giant and dwarf rattlesnakes revealed patterns consistent with shifts to larger and smaller prey, respectively.

Conclusions/Significance

Our data provide the first example of a clear relationship between body size and island area in a squamate reptile species; among vertebrates this pattern has been previously documented in few insular mammals. This finding suggests that selection for body size is influenced by changes in community dynamics that are related to graded differences in area over what are otherwise similar bioclimatic conditions. We hypothesize that in this system shifts to larger prey, episodic saturation and depression of primary prey density, and predator release may have led to insular gigantism, and that shifts to smaller prey and increased reproductive efficiency in the presence of intense intraspecific competition may have led to insular dwarfism.     

Genetic differentiation and demographic history in Drosophila pachea from the Sonoran Desert

Genetic variation at six microsatellite DNA loci and a segment of the mitochondrial cytochrome oxidase subunit I (COI) locus was used to estimate gene flow, population structure, and demographic history in the cactophilic Drosophila pachea from the Sonoran Desert of North America, a species that shows a strict association with its senita host cactus (genus Lophocereus). For microsatellite analyses, thirteen populations of D. pachea were sampled, five in mainland Mexico and the southwestern USA, and eight on the Baja California (Baja) peninsula, covering essentially the entire range of the species. Analysis of molecular variance (AMOVA) of microsatellite data revealed that populations from both the mainland and the Baja peninsula generally showed little structure, although there were a few exceptions, suggesting some local differentiation and restriction of gene flow within both regions. Pairwise comparisons of F(ST) among each of the mainland and Baja populations showed evidence of both panmixia and population subdivision. AMOVA performed on grouped populations from both the mainland and Baja, however, revealed significant partitioning of genetic variation among the two regions, but no partitioning among localities within each region. Bayesian skyline analyses of the COI data set, consisting of four mainland and seven peninsular populations, revealed population expansions dating to the Pleistocene or late Pliocene in D. pachea from both regions, although regional differences were seen in the estimated timing of the expansions and in changes in effective population size over time.     

Island biogeography of bats in Baja California, Mexico: patterns of bat species richness in a near-shore archipelago

Aim We studied the relationship between the size and isolation of islands and bat species richness in a near‐shore archipelago to determine whether communities of vagile mammals conform to predictions of island biogeography theory. We compared patterns of species richness in two subarchipelagos to determine whether area per se or differences in habitat diversity explain variations in bat species richness. Location Islands in the Gulf of California and adjacent coastal habitats on the Baja California peninsula in northwest Mexico. Methods Presence–absence surveys for bats were conducted on 32 islands in the Gulf of California using acoustic and mist‐net surveys. We sampled for bats in coastal habitats of four regions of the Baja peninsula to characterize the source pool of potential colonizing species. We fitted a semi‐log model of species richness and multiple linear regression and used Akaike information criterion model selection to assess the possible influence of log₁₀ area, isolation, and island group (two subarchipelagos) on the species richness of bats. We compared the species richness of bats on islands with greater vegetation densities in the southern gulf (n = 20) with that on drier islands with less vegetation in the northern gulf (n = 12) to investigate the relationship between habitat diversity and the species richness of bats. Results Twelve species of bats were detected on islands in the Gulf of California, and 15 species were detected in coastal habitats on the Baja peninsula. Bat species richness was related to both area and isolation of islands, and was higher in the southern subarchipelago, which has denser vegetation. Log₁₀ area was positively related to bat species richness, which increased by one species for every 5.4‐fold increase in island area. On average, richness declined by one species per 6.25 km increase in isolation from the Baja peninsula. Main conclusions Our results demonstrate that patterns of bat species richness in a near‐shore archipelago are consistent with patterns predicted by the equilibrium theory of island biogeography. Despite their vagility, bats may be more sensitive to moderate levels of isolation than previously expected in near‐shore archipelagos. Differences in vegetation and habitat xericity appear to be associated with richness of bat communities in this desert ecosystem. Although observed patterns of species richness were consistent with those predicted by the equilibrium theory, similar relationships between species richness and size and isolation of islands may arise from patch‐use decision making by individuals (optimal foraging strategies).     

A time‐calibrated phylogenetic approach to assessing the phylogeography,colonization history and phenotypic evolution of snakes in the Japanese Izu Islands

Aim We infer the biogeography and colonization history of a dispersal‐limited terrestrial vertebrate, the Japanese four‐lined ratsnake (Elaphe quadrivirgata), to reveal the number of times mainland populations have invaded the Izu Archipelago of Japan, the mainland sources of these colonists, and the time‐scale of colonization. We compare these results with those of past studies in an attempt to uncover general biogeographical patterns. Moreover, we briefly examine the significance of colonization history when evaluating the evolution of body size and melanism of the Izu Island E. quadrivirgata populations. Location The Izu Islands (Oshima, Toshima, Niijima, Shikine, Kozu, Tadanae and Mikura), a volcanic archipelago off the Pacific coast of central Japan. Methods We obtained DNA sequences of the mitochondrial cytochrome b gene (1117 base pairs) from 373 individual snakes sampled from seven of the Izu Islands and 25 mainland localities. We employed partitioned Bayesian phylogenetic analyses assuming a relaxed molecular clock to estimate phylogenetic relationships among extant haplotypes and to give an explicit temporal scale to the timing of clade divergence, colonization history and tempo of body‐size evolution. Moreover, we employed model‐based biogeographical analysis to calculate the minimum number of times E. quadrivirgata colonized the Izu Islands. Results We found evidence that three separate regions of the Izu Archipelago have been colonized independently from mainland ancestors within the past 0.58–0.20 Ma. The Izu Peninsula plus Oshima and Mikura were both colonized independently from lineages inhabiting eastern mainland Japan. The Toshima, Niijima, Shikine, Kozu and Tadanae populations all derive from a single colonization from western mainland Japan. Oshima has been subject to three or possibly four colonizations. Main conclusions These results support the hypothesis that the extreme body‐size disparity among island populations of this ratsnake evolved in situ. Moreover, the fact that the dwarf, melanistic population inhabiting Oshima descends from multiple mainland colonization events is evidence of an extremely strong natural selection pressure resulting in the rapid evolution of this unique morphology. These results contrast with theoretical predictions that natural selection pressures should play a decreased role on islands close to the mainland and/or subject to frequent or recent immigration.     

TESTING FOR UNEQUAL AMOUNTS OF EVOLUTION IN A CONTINUOUS CHARACTER ON DIFFERENT BRANCHES OF A PHYLOGENETIC TREE USING LINEAR AND SQUARED-CHANGE PARSIMONY: AN EXAMPLE USING LESSER ANTILLEAN ANOLIS LIZARDS

Although a large body of work investigating tests of correlated evolution of two continuous characters exists, hypotheses such as character displacement are really tests of whether substantial evolutionary change has occurred on a particular branch or branches of the phylogenetic tree. In this study, we present a methodology for testing such a hypothesis using ancestral character state reconstruction and simulation. Furthermore, we suggest how to investigate the robustness of the hypothesis test by varying the reconstruction methods or simulation parameters. As a case study, we tested a hypothesis of character displacement in body size of Caribbean Anolis lizards. We compared squared-change, weighted squared-change, and linear parsimony reconstruction methods, gradual Brownian motion and speciational models of evolution, and several resolution methods for linear parsimony. We used ancestor reconstruction methods to infer the amount of body size evolution, and tested whether evolutionary change in body size was greater on branches of the phylogenetic tree in which a transition from occupying a single-species island to a two-species island occurred. Simulations were used to generate null distributions of reconstructed body size change. The hypothesis of character displacement was tested using Wilcoxon Rank-Sums. When tested against simulated null distributions, all of the reconstruction methods resulted in more significant P-values than when standard statistical tables were used. These results confirm that P-values for tests using ancestor reconstruction methods should be assessed via simulation rather than from standard statistical tables. Linear parsimony can produce an infinite number of most parsimonious reconstructions in continuous characters. We present an example of assessing the robustness of our statistical test by exploring the sample space of possible resolutions. We compare ACCTRAN and DELTRAN resolutions of ambiguous character reconstructions in linear parsimony to the most and least conservative resolutions for our particular hypothesis.     

The effect of activity on oxygen consumption,oxygen debt,and heart rate in the lizardsVaranus gouldii andsauromalus hispidus

Summary Oxygen consumption and heart rate were measured during rest and activity in the lizardsVaranus gouldii andSauromalus hispidus. Oxygen debt was calculated from postactive oxygen consumption. Standard metabolic rates of the two animals are similar butVaranus consumes much more oxygen during activity than doesSauromalus (Fig. 1–3). The latter has a constant active metabolic rate above 30 ° C and accumulates a large oxygen debt, which is repayed slowly (Fig. 4).Varanus recovers rapidly from activity (Fig. 5), presumably because of the smaller lactacid debt incurred. Heart rate increment inSauromalus is high (Fig. 8). This variable cannot be responsible for the limitation of active oxygen consumption; calculations of oxygen pulse suggest that an inability to increase A-V difference and/or stroke volume are implicated (Fig. 9).Varanus have evolved mechanisms to sustain high levels of oxygen consumption superior to those of other reptiles investigated. The role of anaerobiosis in the biology of both animals is discussed.     

Dimorphism and divergence in island and mainland Anoles

Relative to the West Indies, the ecology and evolution of anoles inhabiting islands off Central and South America have received little attention. The paucity of studies on continental islands has limited our ability to generalize and extend results based on the West Indian paradigm, as well as our understanding of the profound differences between the adaptive radiations of continental vs. Greater Antillean anoles. Here we compare the morphological, ecological, behavioural and genetic divergence between Anolis nebulosus populations inhabiting a small island in the Bay of Chamela, Mexico, and a nearby mainland forest. Notably, the two populations exhibit intra‐sexual dimorphism with respect to head and limb sizes, the first such polymorphism documented for an Anolis species. We also compare the shape of island and mainland A. nebulosus with each other, the six West Indian ecomorphs and a hypothetical generalist species. Finally, we address the generalist convergence hypothesis for anoles on single species islands. We conclude that convergence on a generalist morphology is widespread among solitary anoles in the West Indies. We present data on a limited sample of solitary anoles with mainland ancestors that suggest a parallel convergence on a similar generalist morphology, probably due to similar adaptive landscapes shaped by selective forces common to small island environments.     

SELECTION FOR SEXUAL ISOLATION BETWEEN GEOGRAPHIC FORMS OF DROSOPHILA MOJAVENSIS. I. INTERACTIONS BETWEEN THE SELECTED FORMS

Drosophila mojavensis comprises three geographic forms occurring in the United States, the Baja California peninsula, and mainland Mexico. Peninsular and mainland forms were selected for increased sexual isolation from each other, while controls were maintained with maximum outbreeding. Response to selection was highly asymmetrical in that isolation was very high between selected peninsular males and mainland females, but nonexistent between selected mainland males and peninsular females. The heightened isolation is primarily due to some change in the peninsular males.     

An example of phenotypic adherence to the island rule? – Anticosti gray jays are heavier but not structurally larger than mainland conspecifics

The island rule refers to the tendency of small vertebrates to become larger when isolated on islands and the frequent dwarfing of large forms. It implies genetic control, and a necessary linkage, of size and body‐mass differences between insular and mainland populations. To examine the island rule, we compared body size and mass of gray jays (Perisoreus canadensis) on Anticosti Island, Québec, located in the Gulf of St. Lawrence, with three mainland populations (2 in Québec and 1 in Ontario). Although gray jays on Anticosti Island were ca 10% heavier, they were not structurally larger, than the three mainland populations. This suggests that Anticosti jays are not necessarily genetically distinct from mainland gray jays and that they may have achieved their greater body masses solely through packing more mass onto mainland‐sized body frames. As such, they may be the first‐known example of a proposed, purely phenotypic initial step in the adherence to the island rule by an insular population. Greater jay body mass is probably advantageous in Anticosti's high‐density, intensely competitive social environment that may have resulted from the island's lack of mammalian nest predators.     

Population morphometric variation of the endemic freshwater killifish, <Emphasis Type="Italic">Fundulus lima</Emphasis> (Teleostei: Fundulidae), and its coastal relative <Emphasis Type="Italic">F. parvipinnis</Emphasis> from the Baja California Peninsula,Mexico

The population morphometric variation of the endangered freshwater killifish (Fundulus lima) was evaluated and compared with that of its euryhaline coastal relatives (F. parvipinnis parvipinnis and F. p. brevis) on the basis of 384 specimens from the Baja California peninsula, Mexico. Forty five standardized body distances were compared by means of discriminant function analysis (DFA). Sixteen body distances were significant to distinguish two groups of populations for F. lima: a first group represented by the Bebelamas and San Javier basins, and second group composed by the basins of San Ignacio, La Purísima, San Luis, San Pedro and Las Pocitas. When all freshwater and coastal populations were compared, the southernmost population of F. lima (Las Pocitas) showed a higher morphometric similarity with the southern coastal subspecies (F. p. brevis), while another southern population (San Pedro) had an intermediate position between the freshwater and coastal forms. This study suggests the presence of five evolutionary units (three freshwater and two coastal) for the genus Fundulus in the Baja California peninsula.     

Relative effects of climate change, isolation and competition on body-size evolution in the Japanese field mouse, Apodemus argenteus

Aim This paper examines body size variation in both recent and Quaternary populations of the Japanese field mouse Apodemus argenteus in order to assess the relative effects on body size of climate change, isolation and competitive interactions with its congeneric A. speciosus. Both temporal (since the Last Glacial Maximum, LGM) and spatial (over the Japanese archipelago) scales are considered. Location The small field mouse is widespread in Japan, and the specimens examined were collected from 10 localities on islands of widely differing area (from 4 km² to 230,510 km²) and at latitudes ranging from 30.3° N to 45.1° N. Methods The effects of geographical factors such as latitude and island area on the size variation of A. argenteus were investigated, using the lower incisor size. In addition, the size of some specimens from two Quaternary localities was compared with the size of the extant specimens. Evolutionary rates of size change since the LGM were calculated in darwins. Hutchinson size ratios were used to examine the pattern of variation of the size segregation between the two Japanese field mice, A. argenteus and A. speciosus, in relation to time and space. Results There was a negative relationship between size and latitude among living A. argenteus populations. In addition, there was no effect of island area on body size, especially at higher latitudes. At lower latitudes, A. argenteus were larger on smaller islands, although this trend was not statistically significant. Quaternary specimens of A. argenteus were smaller in size than their living representatives. The interspecific size ratio between the two Japanese Apodemus was larger on smaller islands and at higher latitudes, and there has been a decrease in the size ratio between the two Apodemus since the LGM. Lastly, in accordance with the theory of character displacement, the small A. argenteus was larger in allopatry than in sympatry, whereas the large A. speciosus was smaller in allopatry than in sympatry. Main conclusions These results indicate that A. argenteus does not conform to Bergmann's rule or to the island rule. The variation in size for the small Japanese field mouse at both spatial and temporal scales may be related to climate change, with an additional effect of competition with the large field mouse, especially on smaller islands. The size convergence between the two Japanese Apodemus observed over the last 21,000 years may be explained by the diminution of available food resources due to the reduction of land mass areas following the LGM. It may also be the result of an evolution towards an optimal body size; a hypothesis previously proposed to explain the evolution of body size in island mammals. Lastly, the evolutionary rates of body size calculated for A. argenteus since the LGM are typical of rates calculated for other Quaternary mainland mammals, thus suggesting that the evolution in this species was not particularly rapid, as is often thought for island mammals.     

GEOGRAPHICAL CORRELATION OF MORPHOLOGICAL VARIATION IN SILVETIA COMPRESSA (FUCACEAE,FUCALES, PHAEOPHYCEAE)

Silvetia compressa ( J. Agardh) Serrão et al. is a common member of the upper intertidal fucoid community on the Pacific coast of America from Humboldt County, California, to Punta Baja, Baja California, Mexico. A relatively narrow range of morphological variability is exhibited by most mainland populations, regardless of latitude, but some mainland populations and all insular populations participate in a complex pattern that we have attempted to analyze. A few populations on the Monterey Peninsula in which the fronds are atypically delicate were described by Setchell & Gardner as f. gracilis, to which was assigned a population from Santa Catalina Island. After comparing populations from various parts of the range of the species, including all of the Channel Islands, we conclude that two subspecies may be recognized. In subsp. compressa, which includes f. gracilis as a growth form and occurs chiefly on the mainland, the frond is robust with long tapered receptacles. In the variant subspecies, which is chiefly insular but also occurs on the coast of northern Baja California, the typical frond has slender axes as in f. gracilis, but is more densely branched and has short ellipsoidal receptacles. Comparison of nucleotide sequences from the ITS regions of rDNA revealed an identical pattern for subsp. compressa from Baja California and central California, including populations assignable to f. gracilis. By contrast, the pattern for the variant subspecies differed by 2 bp (0.3%) from that of subsp. compressa.     

Size evolution in island lizards

Aim  The island rule, small animal gigantism and large animal dwarfism on islands, is a topic of much recent debate. While size evolution of insular lizards has been widely studied, whether or not they follow the island rule has never been investigated. I examined whether lizards show patterns consistent with the island rule.
Location  Islands worldwide.
Methods  I used literature data on the sizes of island–mainland population pairs in 59 species of lizards, spanning the entire size range of the group, and tested whether small insular lizards are larger than their mainland conspecifics and large insular lizards are smaller. I examined the influence of island area, island isolation, and dietary preferences on lizard size evolution.
Results  Using mean snout–vent length as an index of body size, I found that small lizards on islands become smaller than their mainland conspecifics, while large ones become larger still, opposite to predictions of the island rule. This was especially strong in carnivorous lizards; omnivorous and herbivorous species showed a pattern consistent with the island rule but this result was not statistically significant. No trends consistent with the island rule were found when maximum snout–vent length was used. Island area had, at best, a weak effect on body size. Using maximum snout–vent length as an index of body size resulted in most lizard populations appearing to be dwarfed on islands, but no such pattern was revealed when mean snout–vent length was used as a size index.
Main conclusions  I suggest that lizard body size is mostly influenced by resource availability, with large size allowing some lizard populations to exploit resources that are unavailable on the mainland. Lizards do not follow the island rule. Maximum snout–vent length may be biased by sampling effort, which should be taken into account when one uses this size index.     

Model-based comparisons of phylogeographic scenarios resolve the intraspecific divergence of cactophilic Drosophila mojavensis

The cactophilic fly Drosophila mojavensis exhibits considerable intraspecific genetic structure across allopatric geographic regions and shows associations with different host cactus species across its range. The divergence between these populations has been studied for more than 60years, yet their exact historical relationships have not been resolved. We analysed sequence data from 15 intronic X-linked loci across populations from Baja California, mainland Sonora-Arizona and Mojave Desert regions under an isolation-with-migration model to assess multiple scenarios of divergence. We also compared the results with a pre-existing sequence data set of eight autosomal loci. We derived a population tree with Baja California placed at its base and link their isolation to Pleistocene climatic oscillations. Our estimates suggest the Baja California population diverged from an ancestral Mojave Desert/mainland Sonora-Arizona group around 230,000-270,000years ago, while the split between the Mojave Desert and mainland Sonora-Arizona populations occurred one glacial cycle later, 117,000-135,000years ago. Although we found these three populations to be effectively allopatric, model ranking could not rule out the possibility of a low level of gene flow between two of them. Finally, the Mojave Desert population showed a small effective population size, consistent with a historical population bottleneck. We show that model-based inference from multiple loci can provide accurate information on the historical relationships of closely related groups allowing us to set into historical context a classic system of incipient ecological speciation.     

The relationship of terpene composition,morphology, and distribution of populations of Bursera microphylla (Burseraceae)

On the basis of terpene composition, populations ofB. microphylla show north to south affinities on both the Baja California peninsula and the northwest coast of Mexico. The lack of east to west population affinities corresponds with the presumed absence of land connections between the peninsula and mainland throughout the history of this taxon. Morphological similarities between populations in an east-west direction are explained on the basis of contemporary parallel selective influences and not by the closeness of relationship.     

Phylogeography of Supralittoral Rocky Intertidal Ligia Isopods in the Pacific Region from Central California to Central Mexico

Background

Ligia isopods are widely distributed in the Pacific rocky intertidal shores from central California to central Mexico, including the Gulf of California. Yet, their biological characteristics restrict them to complete their life cycles in a very narrow range of the rocky intertidal supralittoral. Herein, we examine phylogeographic patterns of Ligia isopods from 122 localities between central California and central Mexico. We expect to find high levels of allopatric diversity. In addition, we expect the phylogeographic patterns to show signatures of past vicariant events that occurred in this geologically dynamic region.

Methodology/Principal Findings

We sequenced two mitochondrial genes (Cytochrome Oxidase I and 16S ribosomal DNA). We conducted Maximum Likelihood and Bayesian phylogenetic analyses. We found many divergent clades that, in general, group according to geography. Some of the most striking features of the Ligia phylogeographic pattern include: (1) deep mid-peninsular phylogeographic breaks on the Pacific and Gulf sides of Baja peninsula; (2) within the Gulf lineages, the northern peninsula is most closely related to the northern mainland, while the southern peninsula is most closely related to the central-southern mainland; and, (3) the southernmost portion of the peninsula (Cape Region) is most closely related to the southernmost portion of mainland.

Conclusions/Significance

Our results shed light on the phylogenetic relationships of Ligia populations in the study area. This study probably represents the finest-scale phylogeographic examination for any organism to date in this region. Presence of highly divergent lineages suggests multiple Ligia species exist in this region. The phylogeographic patterns of Ligia in the Gulf of California and Baja peninsula are incongruent with a widely accepted vicariant scenario among phylogeographers, but consistent with aspects of alternative geological hypotheses and phylo- and biogeographic patterns of several other taxa. Our findings contribute to the ongoing debate regarding the geological origin of this important biogeographic region.     

Insights into population genetics and evolution of polyploids and their ancestors

We have developed the first comprehensive simulator for polyploid genomes (PolySim) and demonstrated its value by performing large‐scale simulations to examine the effect of different population parameters on the evolution of polyploids. PolySim is unlimited in terms of ploidy, population size or number of simulated loci. Our process considered the evolution of polyploids from diploid ancestors, polysomic inheritance, inbreeding, recombination rate change in polyploids and gene flow from lower to higher ploidies. We compared the number of segregating single nucleotide polymorphisms, minor allele frequency, heterozygosity, R² and average kinship relatedness between different simulated scenarios, and to real data from polyploid species. As expected, allotetraploid populations showed no difference from their ancestral diploids when population size remained constant and there was no gene flow or multivalent (MV) pairing between subgenomes. Autotetraploid populations showed significant differences from their ancestors for most parameters and diverged from their ancestral populations faster than allotetraploids. Autotetraploids can have significantly higher heterozygosity, relatedness and extended linkage disequilibrium compared with allotetraploids. Interestingly, autotetraploids were more sensitive to increasing selfing rate and decreasing population size. MV formation can homogenize allotetraploid subgenomes, but this homogenization requires a higher MV rate than previously proposed. Our results can be considered as the first building block to understand polyploid population evolutionary dynamics. PolySim can be used to simulate a wide variety of polyploid organisms that mimic empirical populations, which, in combination with quantitative genetics tools, can be used to investigate the power of genomewide association, genomic selection or breeding programme designs in these species.