Signals of differential introgression in the genome of natural hybrids of Caribbean anoles

Hybridization facilitates recombination between divergent genetic lineages and can be shaped by both neutral and selective processes. Upon hybridization, loci with no net fitness effects introgress randomly from parental species into the genomes of hybrid individuals. Conversely, alleles from one parental species at some loci may provide a selective advantage to hybrids, resulting in patterns of introgression that do not conform to random expectations. We investigated genomic patterns of differential introgression in natural hybrids of two species of Caribbean anoles, Anolis pulchellus and A. krugi in Puerto Rico. Hybrids exhibit A. pulchellus phenotypes but possess A. krugi mitochondrial DNA, originated from multiple, independent hybridization events, and appear to have replaced pure A. pulchellus across a large area in western Puerto Rico. Combining genome-wide SNP datasets with bioinformatic methods to identify signals of differential introgression in hybrids, we demonstrate that the genomes of hybrids are dominated by pulchellus-derived alleles and show only 10%-20% A. krugi ancestry. The majority of A. krugi loci in hybrids exhibit a signal of non-random differential introgression and include loci linked to genes involved in development and immune function. Three of these genes (delta like canonical notch ligand 1, jagged1 and notch receptor 1) affect cell differentiation and growth and interact with mitochondrial function. Our results suggest that differential non-random introgression for a subset of loci may be driven by selection favouring the inheritance of compatible mitochondrial and nuclear-encoded genes in hybrids.

A biographical account of John Paul Richard Thomas, the man who leaves no stone unturned

This biographical account summarizes the professional career and scientific contributions of John Paul Richard Thomas, a contemporary leading figure in the systematics of West Indian amphibians and non-avian reptiles, especially of blind snakes of the families Typhlopidae and Leptotyphlopidae. Since his first expedition to the West Indies in 1957, Richard's vast field experience (including three trips to Peru between 1968 and 1974), impressive collecting skills, and remarkable ability to detect phenotypic variation among natural populations have resulted in the description of more than 70 species of snakes (24 typhlopids, 4 leptotyphlopids), lizards, and frogs in 16 genera and 11 taxonomic families. Richard joined the faculty of the Department of Biology, University of Puerto Rico, Río Piedras, in 1976 and ever since his efforts significantly advanced organismal biology research at the institution. Although primarily a systematist, his desire to understand multiple aspects of an organism's biology and contagious passion for becoming intimately familiar with animals in their natural environments provided his students the opportunity to conduct research in fields such as behavioral and evolutionary ecology. Richard's mentoring fostered the scientific interests of his graduate students, who were exposed first-hand to every aspect of research, an invaluable experience that served as a springboard for the development of their professional careers inside and outside academia. This Commentary is a fitting tribute to an influential, unassuming scientist whose passion for turning over rocks has led to the discovery of many interesting species.

ORIGINS AND GENETIC DIVERSITY OF INTRODUCED POPULATIONS OF THE PUERTO RICAN RED-EYED COQUÍ, ELEUTHERODACTYLUS ANTILLENSIS, IN SAINT CROIX (U.S. VIRGIN ISLANDS) AND PANAMÁ

The Red-eyed Coquí, Eleutherodactylus antillensis, is a terrestrial frog endemic to the Puerto Rican Bank (Puerto Rico and numerous islands and cays off its eastern coast), in the eastern Caribbean Sea. The species was likely introduced in Saint Croix, an island c. 100 km southeast of Puerto Rico, in the late 1930s, and in Panamá City, Panamá, in the late 1950s or early 1960s, but the source(s) of these introductions are unknown. We analyzed sequence data from one mtDNA locus and four nuDNA introns to infer the origin(s) of the Saint Croix and Panamá City populations and quantify their genetic diversity. Saint Croix and Panamanian populations do not share any haplotypes, and they cluster with different native populations, suggesting that they are derived from separate sources in the Puerto Rican Bank. Patterns of population structure trace the probable sources of E. antillensis in Saint Croix to islands off Puerto Rico's eastern coast, which include Vieques, Culebra, Saint Thomas, Saint John, Tortola, and Virgin Gorda, and possibly to eastern Puerto Rico as well. In contrast, Panamá City E. antillensis probably originated from either western or eastern Puerto Rico. Genetic diversity in the introduced populations is similar to or lower than in populations in the species' native range, indicating that genetic diversity has not increased in the alien frogs. Our findings may facilitate the development of preventive measures to minimize introductions of non-native amphibians in the Caribbean and Central America.

Climate as a driver of tropical insular diversity: comparative phylogeography of two ecologically distinctive frogs in Puerto Rico

The effects of late Quaternary climate on distributions and evolutionary dynamics of insular species are poorly understood in most tropical archipelagoes. We used ecological niche models under past and current climate to derive hypotheses regarding how stable climatic conditions shaped genetic diversity in two ecologically distinctive frogs in Puerto Rico. Whereas the Mountain Coquí, Eleutherodactylus portoricensis, is restricted to montane forest in the Cayey and Luquillo Mountains, the Red-eyed Coquí, E. antillensis, is a habitat generalist distributed across the entire Puerto Rican Bank (Puerto Rico and the Virgin Islands, excluding St. Croix). To test our hypotheses, we conducted phylogeographic and population genetic analyses based on mitochondrial and nuclear loci of each species across their range in Puerto Rico. Patterns of population differentiation in E. portoricensis, but not in E. antillensis, supported our hypotheses. For E. portoricensis, these patterns include: individuals isolated by long-term unsuitable climate in the Río Grande de Loíza Basin in eastern Puerto Rico belong to different genetic clusters; past and current climate strongly predicted genetic differentiation; and Cayey and Luquillo Mountains populations split prior to the last interglacial. For E. antillensis, these patterns include: genetic clusters did not fully correspond to predicted long-term unsuitable climate; and past and current climate weakly predicted patterns of genetic differentiation. Genetic signatures in E. antillensis are consistent with a recent range expansion into western Puerto Rico, possibly resulting from climate change and anthropogenic influences. As predicted, regions with a large area of long-term suitable climate were associated with higher genetic diversity in both species, suggesting larger and more stable populations. Finally, we discussed the implications of our findings for developing evidence-based management decisions for E. portoricensis, a taxon of special concern. Our findings illustrate the role of persistent suitable climatic conditions in promoting the persistence and diversification of tropical island organisms.

Genetic divergence and diversity in the Mona and Virgin Islands Boas, Chilabothrus monensis (Epicrates monensis) (Serpentes: Boidae), West Indian snakes of special conservation concern

Habitat fragmentation reduces the extent and connectivity of suitable habitats, and can lead to changes in population genetic structure. Limited gene flow among isolated demes can result in increased genetic divergence among populations, and decreased genetic diversity within demes. We assessed patterns of genetic variation in the Caribbean boa Chilabothrus monensis (Epicrates monensis) using two mitochondrial and seven nuclear markers, and relying on the largest number of specimens of these snakes examined to date. Two disjunct subspecies of C. monensis are recognized: the threatened C. m. monensis, endemic to Mona Island, and the rare and endangered C. m. granti, which occurs on various islands of the Puerto Rican Bank. Mitochondrial and nuclear markers revealed unambiguous genetic differences between the taxa, and coalescent species delimitation methods indicated that these snakes likely are different evolutionary lineages, which we recognize at the species level, C. monensis and C. granti. All examined loci in C. monensis (sensu stricto) are monomorphic, which may indicate a recent bottleneck event. Each population of C. granti exclusively contains private mtDNA haplotypes, but five of the seven nuclear genes assayed are monomorphic, and nucleotide diversity is low in the two remaining markers. The faster pace of evolution of mtDNA possibly reflects the present-day isolation of populations of C. granti, whereas the slower substitution rate of nuDNA may instead mirror the relatively recent episodes of connectivity among the populations facilitated by the lower sea level during the Pleistocene. The small degree of overall genetic variation in C. granti suggests that demes of this snake could be managed as a single unit, a practice that would significantly increase their effective population size.

Hot and not-so-hot females: reproductive state and thermal preferences of female Arizona Bark Scorpions (Centruroides sculpturatus)

For ectotherms, environmental temperatures influence numerous life history characteristics, and the body temperatures (Tb ) selected by individuals can affect offspring fitness and parental survival. Reproductive trade-offs may therefore ensue for gravid females, because temperatures conducive to embryonic development may compromise females' body condition. We tested whether reproduction influenced thermoregulation in female Arizona Bark Scorpions (Centruroides sculpturatus). We predicted that gravid females select higher Tb and thermoregulate more precisely than nonreproductive females. Gravid C. sculpturatus gain body mass throughout gestation, which exposes larger portions of their pleural membrane, possibly increasing their rates of transcuticular water loss in arid environments. Accordingly, we tested whether gravid C. sculpturatus lose water faster than nonreproductive females. We determined the preferred Tb of female scorpions in a thermal gradient and measured water loss rates using flow-through respirometry. Gravid females preferred significantly higher Tb than nonreproductive females, suggesting that gravid C. sculpturatus alter their thermoregulatory behaviour to promote offspring fitness. However, all scorpions thermoregulated with equal precision, perhaps because arid conditions create selective pressure on all females to thermoregulate effectively. Gravid females lost water faster than nonreproductive animals, indicating that greater exposure of the pleural membrane during gestation enhances the desiccation risk of reproductive females. Our findings suggest that gravid C. sculpturatus experience a trade-off, whereby selection of higher Tb and increased mass during gestation increase females' susceptibility to water loss, and thus their mortality risk. Elucidating the mechanisms that influence thermal preferences may reveal how reproductive trade-offs shape the life history of ectotherms in arid environments.

Reproductive tradeoff limits the predatory efficiency of female Arizona Bark Scorpions (Centruroides sculpturatus)

Background

Life history tradeoffs may result from temporal and physiological constraints intrinsic to an organism. When faced with limited time and energy, compromises occur and these resources are allocated among essential activities, such as body growth, maintenance, foraging, mating, and offspring care. We investigated potential tradeoffs that may occur between reproductive activities and feeding performance in female Arizona Bark Scorpions (Centruroides sculpturatus) by comparing the time taken to capture prey between non-reproductive and reproductive females (gravid females and females exhibiting maternal care, i.e. carrying offspring on their backs).

Results

Gravid females were as efficient at catching prey as non-gravid females. To control for variation in the duration of the maternal care period, we removed all offspring from all post-parturient females after 5 days. Brooding females and females 24 hours following offspring removal (FOR) did not successfully capture prey within the 900-second trial period. Twenty-eight days FOR, females caught prey faster than females displaying maternal care and females 24 hours FOR, but were not as efficient at catching prey as non-gravid and gravid females. When pursuing prey, C. sculpturatus exhibiting maternal care used an active foraging strategy more frequently than non-gravid, gravid, and females 28 days FOR. In contrast, non-gravid, gravid, and females 28 days FOR used active and ambush foraging with similar frequency.

Conclusions

Our data suggest that reproduction does not significantly reduce the predatory efficiency of gravid C. sculpturatus, and that these females can cope with increasing body mass and the physiological costs of gestation. However, the observation that brooding females and females 24 hours FOR did not catch prey within the trial period indicates that maternal care significantly reduces predatory efficiency in these scorpions. Females 28 days FOR were still not as efficient at catching prey as non-gravid and gravid females, suggesting that reproductive costs extend for at least 4 weeks after the end of the maternal care period. Preferential use of an active foraging strategy by brooding females may increase prey encounter rates, allowing the scorpions to more rapidly replenish energy reserves depleted during reproduction. However, active foraging may be energetically costly and increase predation risk for brooding females. Our findings regarding antagonistic interactions between reproduction and feeding in female C. sculpturatus demonstrate the pervasive nature of reproductive costs for viviparous females, and may provide insight on factors that influence the diversity of reproductive strategies observed in nature.

Genetic drift or natural selection? Hybridization and asymmetric mitochondrial introgression in two Caribbean lizards (Anolis pulchellus and Anolis krugi)

Hybridization and gene introgression can occur frequently between closely related taxa, but appear to be rare phenomena among members of the species-rich West Indian radiation of Anolis lizards. We investigated the pattern and possible mechanism of introgression between two sister species from Puerto Rico, Anolis pulchellus and Anolis krugi, using mitochondrial (ND2) and nuclear (DNAH3, NKTR) DNA sequences. Our findings demonstrated extensive introgression of A. krugi mtDNA (k-mtDNA) into the genome of A. pulchellus in western Puerto Rico, to the extent that k-mtDNA has mostly or completely replaced the native mtDNA of A. pulchellus on this part of the island. We proposed two not mutually exclusive scenarios to account for the interspecific matings between A. pulchellus and A. krugi. We inferred that hybridization events occurred independently in several populations, and determined that k-mtDNA haplotypes harboured in individuals of A. pulchellus can be assigned to four of the five major mtDNA clades of A. krugi. Further, the spatial distribution of k-mtDNA clades in the two species is largely congruent. Based on this evidence, we concluded that natural selection was the probable driving mechanism for the extensive k-mtDNA introgression into A. pulchellus. Our two nuclear data sets yielded different results. DNAH3 showed reciprocal monophyly of A. pulchellus and A. krugi, indicating no effect of hybridization on this marker. In contrast, the two species shared nine NKTR alleles, probably due to incomplete lineage sorting. Our study system will provide an excellent opportunity to experimentally assess the behavioural and ecological mechanisms that can lead to hybridization in closely related taxa.

Sea level, topography and island diversity: phylogeography of the Puerto Rican Red-eyed Coquí, Eleutherodactylus antillensis

Quaternary climatic oscillations caused changes in sea level that altered the size, number and degree of isolation of islands, particularly in land-bridge archipelagoes. Elucidating the demographic effects of these oscillations increases our understanding of the role of climate change in shaping evolutionary processes in archipelagoes. The Puerto Rican Bank (PRB) (Puerto Rico and the Eastern Islands, which comprise Vieques, Culebra, the Virgin Islands and associated islets) in the eastern Caribbean Sea periodically coalesced during glaciations and fragmented during interglacial periods of the quaternary. To explore population-level consequences of sea level changes, we studied the phylogeography of the frog Eleutherodactylus antillensis across the archipelago. We tested hypotheses encompassing vicariance and dispersal narratives by sequencing mtDNA (c. 552 bp) of 285 individuals from 58 localities, and four nuDNA introns (totalling c. 1633 bp) from 173 of these individuals. We found low support for a hypothesis of divergence of the Eastern Islands populations prior to the start of the penultimate interglacial c. 250 kya, and higher support for a hypothesis of colonization of the Eastern Islands from sources in eastern Puerto Rico during the penultimate and last glacial period, when a land bridge united the PRB. The Río Grande de Loíza Basin in eastern Puerto Rico delineates a phylogeographic break. Haplotypes shared between the PRB and St. Croix (an island c. 105 km south-east of this archipelago) likely represent human-mediated introductions. Our findings illustrate how varying degrees of connectivity and isolation influence the evolution of tropical island organisms.

Climatic stability and genetic divergence in the tropical insular lizard Anolis krugi, the Puerto Rican 'Lagartijo Jardinero de la Montaña'

Two factors that can lead to geographic structuring in conspecific populations are barriers to dispersal and climatic stability. Populations that occur in different physiographic regions may be restricted to those areas by physical and/or ecological barriers, which may facilitate the formation of phylogeographic clades. Long-term climatic stability can also promote genetic diversification, because new clades are more likely to evolve in areas that experience lesser climatic shifts. We conducted a phylogeographic study of the Puerto Rican lizard Anolis krugi to assess whether populations of this anole show genetic discontinuities across the species' range, and if they do, whether these breaks coincide with the boundaries of the five physiographic regions of Puerto Rico. We also assessed whether interpopulation genetic distances in A. krugi are positively correlated with relative climatic stability in the island. Anolis krugi exhibits genetic structuring, but the phylogroups do not correspond to the physiographic regions of Puerto Rico. We used climatic reconstructions of two environmental extremes of the Quaternary period, the present conditions and those during the last glacial maximum (LGM), to quantify the degree of climatic stability between sampling locations. We documented positive correlations between genetic distances and relative climatic stability, although these associations were not significant when corrected for autocorrelation. Principal component analyses indicated the existence of climatic niche differences between some phylogeographic clades of A. krugi. The approach that we employed to assess the relationship between climatic stability and the genetic architecture of A. krugi can also be used to investigate the impact of factors such as the spatial distribution of food sources, parasites, predators or competitors on the genetic landscape of a species.

Feeding ecology of the Great Basin Rattlesnake (Crotalus lutosus, Viperidae)

Documenting variation in organismal traits is essential to understanding the ecology of natural populations. We relied on stomach contents of preserved specimens and literature records to assess ontogenetic, intersexual, temporal, and geographic variations in the feeding ecology of the North American Great Basin Rattlesnake ( Crotalus lutosus Klauber, 1930). Snakes preyed mainly on rodents, occasionally on lizards, and less frequently on birds; squamate eggs and frogs were rarely eaten. There was a positive relationship between predator and prey size. The best predictors of this relationship were prey diameter as a function of snake body length and head size, underscoring the importance of prey diameter for gape-limited predators such as snakes. Crotalus lutosus displayed ontogenetic, sexual, and seasonal variations in diet. Smaller rattlesnakes fed predominantly on lizards, whereas larger individuals mostly fed on mammals. Females fed on lizards more often than males. The proportion of mammals in the diet was highest during the summer, a temporal variation that may be related to behavioral shifts in the diel activity and prey selectivity of C. lutosus, and (or) to differential abundance of rodents between seasons. Great Basin Rattlesnakes also displayed geographic variation in feeding habits, with snakes from the Great Basin Desert eating a higher proportion of lizards than serpents from the more northern Columbia Plateau.

Habitat selection by the Puerto Rican yellow-chinned anole,Anolis gundlachi

Habitat selection can directly affect the fitness of an individual and the evolutionary dynamics of the population to which that organism belongs. We studied habitat use of the Puerto Rican yellow-chinned anole (Anolis gundlachi Peters, 1876) to examine whether this arboreal lizard uses its environment in a nonrandom manner. Males and females preferred woody vegetation substrates over nonwoody plants and sierra palms (Prestoea acuminata var. montana (Graham) A. Henderson and G. Galeano) as perching sites, and they also selected wider vegetation than what was randomly available. Selection for minimizing conspicuousness to potential predators and for increased locomotion capacity may help explain the preference for woody substrates and broader surfaces, respectively. Anolis gundlachi relies almost exclusively on visual cues for foraging and social interactions, and using wider perches also increases an individual's ability to scan a larger proportion of its territory. Our findings thus indicate that the nonrandom habitat use of free-ranging A. gundlachi leads to the selection of perching substrates that may increase performance of ecologically relevant capabilities.

Mitochondrial DNA-Based phylogeography of North American rubber boas, Charina bottae (Serpentes: Boidae)

We used 783 bp of mitochondrial DNA sequences to study the phylogeography of Charina bottae (rubber boa) in western North America, with an emphasis on populations from California (U.S.A.). Maximum-parsimony and maximum-likelihood methods identified a basal divergence within C. bottae that corresponds to southern and northern segments of its current distribution. These clades coincide with the ranges of the two recognized subspecies, C. b. umbratica in the south and C. b. bottae to the north. A subsequent cladogenetic event in the C. b. bottae clade resulted in two groupings, which we refer to as the Sierra Nevada and the Northwestern subclades, based on the geographic distribution of their constituent populations. The two subclades have completely allopatric distributions, with a genetic break in the vicinity of Lassen Volcanic National Park in northeastern California, an area that was subjected to glaciation during the Pleistocene and that has been volcanically active in the past 100 years. An earlier genetic study documented fixed differences between populations of bottae and umbratica in four of seven allozymes surveyed, and despite noticeable variation and overlap in the characters that define C. b. bottae and C. b. umbratica, the two forms still can be separated in most cases using a suite of morphological traits. All available evidence thus indicates that C. b. umbratica is a genetically cohesive, allopatric taxon that is morphologically diagnosable, and we conclude that it is an independent evolutionary unit that should be recognized as a distinct species, Charina umbratica.

Molecular systematics of new world gopher, bull, and pinesnakes (Pituophis: Colubridae), a transcontinental species complex

Pituophis melanoleucus (gopher, bull, and pinesnakes) is among the most widely distributed polytypic species complexes in North America, with most authors recognizing from a single transcontinental species (the melanoleucus complex, composed of 15 subspecies) to four (monotypic and polytypic) species. We used mitochondrial gene sequences from the two middle American species, P. deppei and P. lineaticollis, and from 13 subspecies from most of the range of the melanoleucus complex to test various phylogenetic hypotheses for Pituophis. Maximum parsimony and maximum likelihood methods identified the same major clades within Pituophis and indicated that two segments of the melanoleucus complex, the lodingi-melanoleucus-mugitus eastern pinesnake clade and the affinis-annectens-bimaris-catenifer-deserticola- sayi-ruthveni-vertebr alis clade from central and western United States and northern Mexico, represent divergent, allopatric lineages with no known intergradation zone. We recognize each of these two groupings as a different species. Our data also indicate that some ruthveni are more closely related to sayi than to other ruthveni. Nonetheless, ruthveni is an allopatric taxon diagnosable from its closest relatives by a combination of morphometric characters, and because it is likely that at least some of these traits are independent and genetically inherited, we interpret this as evidence that ruthveni has attained the status of independent evolutionary lineage, despite the fact that it retains strong genetic affinities with sayi. The endemic Baja Californian gopher snakes (bimaris and vertebralis) are considered by some taxonomists as a different species, P. vertebralis, but we discovered that these serpents belong to two different clades and hence we do not agree with the recognition of P. vertebralis as presently defined. In summary, we believe that three distinct species are included in the melanoleucus complex, Pituophis melanoleucus (sensu stricto), P. catenifer, and P. ruthveni, and that their recognition better represents the evolutionary diversity within this species complex.

Phylogeography of the California mountain kingsnake, Lampropeltis zonata (Colubridae)

The phylogeography of the California mountain kingsnake, Lampropeltis zonata, was studied using mitochondrial DNA sequences from specimens belonging to the seven recognized subspecies and collected throughout the range of the species. Maximum parsimony and maximum likelihood methods identified a basal split within L. zonata that corresponds to southern and northern segments of its distribution. The southern clade is composed of populations from southern California (USA) and northern Baja California, Mexico. The northern clade is divided into two subclades, a 'coastal' subclade, consisting of populations from the central coast of California and the southern Sierra Nevada Mountains of eastern California, and a 'northeastern' subclade, mainly comprised of populations north of the San Francisco Bay and from the majority of the Sierra Nevada. We suggest that past inland seaways in southwestern California and the embayment of central California constituted barriers to gene flow that resulted in the two deepest divergences within L. zonata. Throughout its evolutionary history, the northern clade apparently has undergone instances of range contraction, isolation, differentiation, and then expansion and secondary contact. Examination of colour pattern variation in 321 living and preserved specimens indicated that the two main colour pattern characters used to define the subspecies of L. zonata are so variable that they cannot be reliably used to differentiate taxonomic units within this complex, which calls into question the recognition of seven geographical races of this snake.