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Molecular analyses confirming the introduction of nile crocodiles, crocodylus niloticus laurenti 1768 (Crocodylidae), in southern Florida, with an assessment of potential for establishment, spread, and impacts
Abstract
Abstract.—The state of Florida, USA, has more introduced herpetofauna than any other governmental region on Earth.
Four species of nonnative crocodilians have been introduced to Florida (all since 1960), one of which is established.
Between 2000–2014 we field-collected three nonnative crocodilians in Miami-Dade County, Florida, and one in Hendry
County, Florida. We used DNA barcoding and molecular phylogenetics to determine species identification and native
range origin. Also, we described diet, movement, and growth for one crocodile. Our molecular analyses illustrated that
two of the crocodiles we collected are most closely related to Nile Crocodiles (Crocodylus niloticus) from South Africa,
suggesting this region as a source population. We, thus, documented the first known introduction of C. niloticus in
Florida. Two, and possibly three of the introduced crocodiles shared the same haplotype, suggesting they are likely from
the same introduction pathway or source. One animal was captured, measured, marked, and released, then recaptured 2
y later allowing us to calculate growth rate (40.5 cm/y) and movement. The most likely route of travel by waterway (i.e.,
canal) illustrates that this animal traveled at least 29 km from its original capture site. One crocodile escaped from a
facility in Hendry County, Florida, and survived in 1,012 ha of semi-wild habitat for three to four years, confirming that
this species can survive in southern Florida.
... Florida harbors the highest diversity of established nonindigenous reptile species in the world, with three turtles, 50 lizards, five snakes, and one crocodilian, most of which arrived through the commercial pet trade (Krysko et al., 2011. Over the last few decades, an increasing number of exotic crocodilian species has been registered in Florida, including Caiman crocodilus, Crocodylus niloticus, Paleosuchus palpebrosus, Paleosuchus trigonatus, and Mecistops cataphractus (Krysko et al., 2011;Rochford et al., 2016). However, only Ca. crocodilus is established in Florida (Ellis, 1980;Krysko et al., 2019). ...
... Recent molecular phylogenetic studies have revealed substantial cryptic lineage diversity within Crocodylia, some of which have been or will likely be recognized as distinct species within Caiman (Roberto et al., 2020), Osteolaemus, Mecistops (Shirley et al., 2014), Crocodylus (Hekkala et al., 2011), and Paleosuschus (Muniz et al., 2018;Bittencourt et al., 2019). Rochford et al. (2016) also employed similar tools to identify introduced individuals of Crocodylus in southern Florida as Cr. niloticus, most likely of South African origins, while previous to this study it was thought the introduced species was the morphologically similar Crocodylus suchus. ...
The state of Florida has the world's highest diversity of established nonnative reptiles, including snakes, lizards, turtles, and crocodilians, most of them introduced from the pet trade. The Spectacled Caiman (Caiman crocodilus) is the only nonnative crocodilian established in Florida, with the earliest date of introduction in 1950. Despite its likely origin being Colombia, the taxonomic identity of the subspecies occurring in Florida remains unknown. We report the first study that resolves the taxonomic status of the population of Ca. crocodilus in Florida based on molecular analysis of samples collected from the 1970s to 2013. We also investigate the probable origin of this population as well as the specimens of the Dwarf Caimans, Paleosuchus palpebrosus and Paleosuchus trigonatus, which have been collected in Florida. We identified only one lineage of Ca. crocodilus in Florida, corresponding to Caiman crocodilus fuscus, and our results indicate the Magdalena River basin in Colombia as the most likely area of origin. We also correct the identification of Paleosuchus recorded in Florida and identify the Guiana Shield, and specifically Guyana, as the most likely region from which these specimens were introduced.
... Outside its' natural range, C. niloticus have been wild-caught and genetically confirmed in southern Florida, USA most likely as either released pets or zoological escapees (Rochford et al. 2016). Rochford et al. (2016) raise concerns about the potential risk of human-crocodile conflicts as well as the potential for hybridization with the indigenous C. acutus population. ...
... Outside its' natural range, C. niloticus have been wild-caught and genetically confirmed in southern Florida, USA most likely as either released pets or zoological escapees (Rochford et al. 2016). Rochford et al. (2016) raise concerns about the potential risk of human-crocodile conflicts as well as the potential for hybridization with the indigenous C. acutus population. Neither risk has so far been realised. ...
Since the last Crocodilus niloticus assessment in 1996, genetic analysis confirmed two lineages of African Crocodylus, namely C. niloticus and C. suchus (Schmitz et al. 2003, Hekkala et al. 2011, Shirley et al. 2015). This assessment takes account of this recent information and only considers the range of C. niloticus (see the distirbution map and the Geographic Range section: 26 countries in southern and eastern Africa). This range represents the majority of habitat and populations on which previous continent-wide assessments of the Nile Crocodile were based. Despite some evidence of localised population declines (Ottley et al. 2008, Fergusson 2010, Bourquin and Leslie 2011, Combrink et al. 2011, Ferreira and Pienaar 2011, Calverley and Downs 2014, Marais 2014, Behangana et al. 2017), C. niloticus (sensu novo) generally remains widespread and as the population has not significantly changed, the assessment LC remains the same. West African populations constituting C. suchus are likely depleted and less numerous and will be assessed separately.
... As part of the introduced reptile fauna, a number of non-native crocodylian species have been recorded in Florida over the last few decades, including the spectacled caiman (Caiman crocodilus), Cuvier's dwarf caiman (Paleosuchus palpebrosus), smoothfronted caiman (P. trigonatus), Nile crocodile (Crocodylus niloticus), and West African slender-snouted crocodile (Mecistops cataphractus; Krysko et al. 2011;Rochford et al. 2016;Roberto et al. 2021). However, only one species-the spectacled caiman (C. ...
The US state of Florida is home to an alarmingly large number of invasive species, many of which have proven detrimental to native ecosystems. Biological invasions of reptiles in particular have been a major concern in recent years. The spectacled caiman (Caiman crocodilus) was first introduced from Latin America to Florida in the 1950’s. Given there are now established breeding populations across southern Florida, there are ongoing efforts to control them. Therefore, there is a need to understand this species’ natural history and introduction pathways. Previous studies have cited the Caribbean Coastal region of Colombia as a primary, and possibly exclusive, origin of C. crocodilus in Florida, and the species was identified as belonging to the C. c. fuscus molecular lineage. However, previous genetic sampling has been limited and may have been biased by small sample sizes and limited geographic scale. We collected 27 genetic samples from caimans captured in Florida, and sequenced the mitochondrial genes, Cytochrome oxidase I (COI) and Cytochrome B (CytB) for comparison with homologous gene fragments available for the species at GenBank. We found genetic evidence for multiple introduction events and the taxonomic classification of the Florida caimans as two distinct molecular lineages (C. c. fuscus and C. c. crocodilus) originating from at least two different regions: the Magdalena River Basin in Colombia and the Upper Branco River Basin in northern Brazil. This study helps to elucidate the genetic history of Florida caimans and provides valuable insight for population management of the species in Florida.
... En un estudio reciente se han localizado en Florida, Estados Unidos, entre dos y tres cocodrilos de Nilo (Crocodylus niloticus). Esto supone una amenaza para los cocodrilos de Florida por la introgresión genética, y se recomienda que siga siendo estudiado por si pudiera haber más de estos cocodrilos y por su impacto (Rochford et al., 2016). 68 situación actual de los grandes depredadores terrestres ...
Se analiza la distribución y en algunos casos abundancia de los grandes depredadores a nivel mundial, así como 3 de estos grandes depredadores en México y algunos temas como etnobiología, y el papel de los zoos en la conservación
... En un estudio reciente se han localizado en Florida, Estados Unidos, entre dos y tres cocodrilos de Nilo (Crocodylus niloticus). Esto supone una amenaza para los cocodrilos de Florida por la introgresión genética, y se recomienda que siga siendo estudiado por si pudiera haber más de estos cocodrilos y por su impacto (Rochford et al., 2016). 68 situación actual de los grandes depredadores terrestres ...
La presente obra es el resultado del Simposio Internacional Biología de la Conservación: Grandes Depredadores de México, organizado por el Cuerpo Académico Consolidado Ecología Conductual y Conservación, Centro de Investigación en Ciencias Biológicas Aplicadas, Universidad Autónoma del Estado de México. En este evento participaron investigadores de 12 instituciones nacionales y una extranjera. Se realizó un análisis de amplio del estado de conservación de 21 especies de grandes depredadores distribuidas en todo el mundo, principalmente grandes mamíferos y reptiles como cocodrilos, su densidad en diversos sitios a nivel mundial y las perspectivas de conservación. Todas las especies analizadas están en alguna categoría de riesgo a nivel internacional.
Como resultado del simposio se evidenció que su conservación es cada vez más crítica, y debemos sumar esfuerzos institucionales (gubernamentales y académicas) así como sociedad en general para llevar a cabo acciones inmediatas para mantener las poblaciones de estos grandes depredadores
... En un estudio reciente se han localizado en Florida, Estados Unidos, entre dos y tres cocodrilos de Nilo (Crocodylus niloticus). Esto supone una amenaza para los cocodrilos de Florida por la introgresión genética, y se recomienda que siga siendo estudiado por si pudiera haber más de estos cocodrilos y por su impacto (Rochford et al., 2016). 68 situación actual de los grandes depredadores terrestres ...
... Case studies from other tropical systems, including the dramatic if poorly understood shift in community structure and lake trophic ecology observed in Lake Victoria following its colonization by Nile perch (Lates niloticus), should serve as a clear warning of the implications of introducing apex predators (Ogutu-Ohwayo, 1990). This trend perhaps reached a new level with the recent discovery of Nile crocodiles (Crocodylus niloticus) in southern Florida (Rochford et al., 2016). ...
Earth's aquatic habitats are some of its most important ecosystems and support populations of many of its most imperilled species. The future demands of Earth's growing human populations will increasingly stress its aquatic resources on multiple spatial and temporal scales, as highlighted by numerous authors when predicting trends in biodiversity in many key aquatic hotspots.
Identifying key stressors and understanding potential linkages between these stressors are important first steps to mitigating human impacts on at‐risk aquatic resources. Here, an overview is provided of the established and emerging threats to aquatic biodiversity at local, regional and global scales, including emerging diseases, expanding influence of invasive species, new industries, and the accelerating trajectory of climate change, as well as perspectives on potential management strategies.
Copyright © 2016 John Wiley & Sons, Ltd.
Romeo and Juliet: a forbidden love story? A review of hybridization in keystone, aquatic
megafauna. Hybridization, understood here as the sexual reproduction between
individuals of different species, is relatively common in riverine, estuarine, and
marine environments. Investigating hybridization in wild populations of aquatic
megafauna species provides important insight into their biology, evolution, and
conservation. Here, we conducted an extensive and systematic review of published
reports of hybrids in keystone, aquatic megafauna, aiming to provide a clear
summary of state-of-the-art and hybridization trends in this group. We selected
129 journal articles reporting 80 hybrids in aquatic megafauna. We included
mammals (40.3 %), turtles (33.3 %), crocodilians (17.8 %), and elasmobranchs
(8.5 %) that are widely distributed in oceans and continental waters. Our results
showed a clear increase in reports of hybrids involving aquatic megafauna in
recent years, possibly reflecting the improvement in molecular techniques. However,
this increase could also be a consequence of translocation of organisms and
habitat modification by humans, and may have a critical impact on conservation,
particularly regarding already depleted populations. Hybridization has directly or
indirectly facilitated the extinction of many species, but it has also played a crucial
role in the evolution and adaptation of many others. To determine whether
hybridization is a natural effect or a collateral effect of anthropic pressures we
need to understand its implications on the conservation of aquatic megafauna.
Around 200 M. niger, mainly 2-3-year-old juveniles, and at least 10 adult/subadults were taken to the Jaguar Conservation Fund/Instituto
Onça-Pintada (IOP) facilities, located in the municipality of Mineiros, Goiás State. It is well known that crocodilians can easily scape from captivity and become established. The potential scape of Black Caimans might involve serious consequences, and result in cascading effect on the ecosystem processes. We believe that this is a serious matter and state and federal institutions in Brazil need to address this subject properly to avoid unnecessary ecological damage.
More nonindigenous species occur in Florida, USA, than any other region worldwide and may threaten many of Florida's natural resources. The frequency of new reports mandates the need for regular updates. Herein, we use photographic and specimen vouchers in addition to literature records to provide updated information on verified nonindigenous amphibians and reptiles in Florida. Between our most recent summary in 2012 and the end of 2015, 38 additional species are known to have been intercepted (n=2) or introduced (n=36). We also update the invasion stage of seven species previously reported from Florida and report that five additional taxa are now established. In total 191 independent known introductions of 180 herpetofaunal taxa led to the establishment of 63 taxa. This suggests that one in three introduced herpetofaunal species becomes established in Florida. The pet trade represents the most common introduction pathway among these species and a single animal importer in Hollywood, Broward County, is the probable source for introduction of a quarter of all herpetofauna introduced to Florida.
Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
The analysis of stomach contents can shed light on patterns of prey availability and foraging habits of a predator; however, recent studies have shown the potential bias in dietary studies resulting from differential digestion rates of various prey items. The stomachs of 286 Nile Crocodiles (17–166 cm snout–vent length) were lavaged over a two-year period. Taking prey residence times into account, the contents were examined for prey eaten within 24 h. Crocodylus niloticus has a similar ontogenetic shift in diet to that of other crocodilians. Yearlings consumed primarily aquatic insecta and arachnida. As crocodile size increased (juveniles), the diet became more diverse including crustacea, amphibia, and fish. The largest size class (subadults) consumed primarily fish. Yearlings fed consistently throughout the year; however a higher proportion of empty stomachs occurred within the juvenile and subadult size classes during the winter months. Seven species of nematodes were found within the stomachs, four of which represent new geographic records.
Management of threatened species with conserved morphology is hindered by misidentification and potential hybridization in captivity. African crocodiles of the genera Osteolaemus, Crocodylus and Mecistops were previously considered monotypic, but have recently been identified as consisting of three, two and two cryptic species, respectively. Mitochondrial cytochrome c oxidase subunit I (COI) new and published sequences from 310 wild-caught specimens were compared with 71 US zoological specimens to identify (barcode) species. We also sequenced either nuclear lactate dehydrogenase A or an anonymous microsatellite flanking sequence in both wild and captive specimens to identify potential first-generation intra-generic hybridization in captive populations. The Osteolaemus COI barcoding gap was 7–9% sequence divergence. In contrast, the two African Crocodylus species had a 4.7% barcoding gap. These results, in addition to a previously published Mecistops barcoding gap (4.9%), support the use of barcoding as a tool for diagnosing African crocodile species in captive populations. Captive individuals from 14 collections in the US represented five of the seven putative African taxa. Nuclear heterozygosity at fixed polymorphisms differentiating species within genera suggested that 23% of the captive Osteolaemus samples were admixed O. tetraspis × O. sp. nov. cf. tetraspis – West Africa, while no ex situ hybrids were found for Crocodylus or Mecistops. Our results underscore the need to formally recognize divergent crocodile taxa, especially in light of regional threats, and for proper captive breeding management.
Tupinambis
merianae, is a large, omnivorous tegu lizard native to South America. Two populations of tegus are established in the state of Florida, USA, but impacts to native species are poorly documented. During summer 2013, we placed automated cameras overlooking one American alligator (Alligator mississippiensis) nest, which also contained a clutch of Florida red-bellied cooter (Pseudemys nelsoni) eggs, and one American crocodile (Crocodylus acutus) nest at a site in southeastern Florida where tegus are established. We documented tegu activity and predation on alligator and turtle eggs at the alligator nest, and tegu activity at the crocodile nest. Our finding that one of the first two crocodilian nests to be monitored was depredated by tegus suggests that tegus should be further evaluated as a threat to nesting reptiles in Florida.
Since removal from the endangered species list, Alligator mississippiensis (American Alligator) populations have recovered to allow regulated harvest throughout most of their range. However, harvest/population management is complicated since alligators are long-lived, reach sexual maturity at a minimum size rather than age, and experience differential growth rates depending on geographic location, growing season length, local environmental conditions, habitat, and population density. To date, few data exist on age, sex, growth, and size structure of inland alligator populations. In this Study, alligator growth rate and condition were qualitified through an intensive mark-recapture Study conducted at Angelina-Neches/Dam
The growth dynamics of the American alligator (Alligator mississippiensis) were studied in the subtropical Florida Everglades using extensive mark-recapture data from over 2000 recaptures of known-aged and unknown-aged animals. A model based on the power curve best describes growth of Everglades alligators. The nonasymptotic character of this curve leads to rejection of the hypothesis that alligator growth is determinate. A model consisting of piece-wise linear equations better described growth in the first year, and suggested a period of arrested growth occurred in the first winter. A comparison of predictions from growth models derived from several populations indicated that Everglades alligators grew more slowly than did those in more temperate areas, leading to the rejection of the hypothesis that growth rates in subtropical Florida would be elevated because of the long growing season. We attribute this result to a combination of increased maintenance costs and a limited resource base in the Everglades.
Analyses considered the extent to which growth model evaluation and use can be affected by data selection. Mathematical constraints posed by negative growth data can be alleviated by including growth records over combined recapture intervals to achieve a positive growth increment. However, periods of no to negative growth may be real, and such deviations are obscured by fitting growth data to monotonically increasing models.
A recent record cold spell in southern Florida (2–11 January 2010) provided an opportunity to evaluate responses of an established
population of Burmese pythons (Python molurus bivittatus) to a prolonged period of unusually cold weather. We observed behavior, characterized thermal biology, determined fate of
radio-telemetered (n=10) and non-telemetered (n=104) Burmese pythons, and analyzed habitat and environmental conditions experienced by pythons during and after a historic
cold spell. Telemetered pythons had been implanted with radio-transmitters and temperature-recording data loggers prior to
the cold snap. Only one of 10 telemetered pythons survived the cold snap, whereas 59 of 99 (60%) non-telemetered pythons for
which we determined fate survived. Body temperatures of eight dead telemetered pythons fluctuated regularly prior to 9 January
2010, then declined substantially during the cold period (9–11 January) and exhibited no further evidence of active thermoregulation
indicating they were likely dead. Unusually cold temperatures in January 2010 were clearly associated with mortality of Burmese
pythons in the Everglades. Some radio-telemetered pythons appeared to exhibit maladaptive behavior during the cold spell,
including attempting to bask instead of retreating to sheltered refugia. We discuss implications of our findings for persistence
and spread of introduced Burmese pythons in the United States and for maximizing their rate of removal.
Keywords
Python molurus
-Florida Everglades-Cold temperatures-Invasive species-Mortality-Thermoregulation
The creation and use of a globally available database of DNA sequences from a standardized gene region has been proposed as
a tool for species identification, assessing genetic diversity and monitoring the legal and illegal trade in wildlife species.
Here, we contribute to the Barcode of Life Data System and test whether a short region of the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene would reliably distinguish among a suite of commonly hunted African and South American mammal and reptile species.
We used universal primers to generate reference barcode sequences of 645bp for 23 species from five vertebrate families (Crocodilidae, Alligatoridae, Bovidae, Suidae and Cercopithecidae). Primer cocktails yielded high quality barcode sequences for 179 out of 204 samples (87.7%) from all species included in
the study. For most taxa, we sequenced multiple individuals to estimate intraspecific sequence variability and document fixed
diagnostic characters for species identification. Polymorphism in the COX1 fragment was generally low (mean=0.24%), while differences between congeneric species averaged 9.77%. Both fixed character
differences and tree-based maximum likelihood distance methods unambiguously identified unknown and misidentified samples
with a high degree of certainty. Barcode sequences also differentiated among newly identified lineages of African crocodiles
and identified unusually high levels of genetic diversity in one species of African duiker. DNA barcoding offers promise as
an effective tool for monitoring poaching and commercial trade in endangered species, especially when investigating semi-processed
or morphologically indistinguishable wildlife products. We discuss additional benefits of barcoding to ecology and conservation.
KeywordsBarcode of life–Caiman–Crocodiles–Cytochrome c oxidase subunit 1 (COX1)–Hunting–Molecular forensics–Primates–Wildlife monitoring–Maximum likelihood phylogeny–Ungulates
Habitat loss and degradation in the Mexican Caribbean, caused by the development of tourism, have decreased the potential nesting area for the American crocodile (Crocodylus acutus) and have fragmented the populations of the Yucatan peninsula. Our study investigated five populations (three continental: North, South, Sian Ka’an, and two insular: Cozumel, Banco Chinchorro) of C. acutus in the Mexican Caribbean using seven different inter simple sequence repeat (ISSR) markers as tools for genetic variability and population differentiation. Three classification methods were tested and compared: distance analysis, self-organizing map, and Bayesian methods, to evaluate the resolution of each method with ISSR markers. The 77 loci selected revealed a high variability between populations (polymorphism from 17% for Sian Ka’an to 75% for Banco Chinchorro) with a total polymorphism of 84% and a global coefficient of gene differentiation (G
ST
) of 0.296, but low values of Nei’s Gene diversity (from 0.065 for Sian Ka’an to 0.233 for Banco Chinchorro). Our results suggest elevated inbreeding in all local populations with higher indices for Banco Chinchorro and lower indices for Sian Ka’an. Three independent classification methods gave similar results, and suggested that most continental individuals are admixtures, with different levels of introgression, with the sympatric species Crocodylus moreletii. We propose that the islands/atolls remain the sole areas with genetically “pure” American crocodiles and we discuss these results for future conservation of this endangered crocodile species.
The American crocodile (Crocodylus acutus) is a large apex predator with an extensive but fragmented range. Crocodylus acutus suffered a population crash and was almost extirpated from Florida (USA) during the 1970s; however, in 2007 it was federally
downlisted from endangered to threatened based on an increase of suitable habitat and a growing population. A genetic assessment
of this population has not been performed even though foreign crocodiles have been released into Florida waters. Herein, we
use mitochondrial and nuclear DNA markers to characterize relationships among American crocodiles along the southern coast
of Florida and reference samples from other countries. We detected inter- and intra-specific hybridization and unexpected
population structure attributed to human-mediated migration of crocodiles from Latin America and the Greater Antilles. Our
results suggest that the population size of crocodiles actually native to Florida should be reevaluated, particularly in light
of ongoing admixture in this population. We reemphasize the utility of genetic markers in conservation and management programs
for endangered species; especially those that can hybridize with closely related congeners. The American crocodile in Florida
has recovered owing to successful conservation initiatives, but a long-term management protocol that takes genetic data into
account is still needed.
Keywords
Crocodylus
–Endangered species recovery–Human-mediated migration–Hybridization–Population genetics
Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
Alligators and crocodiles integrate biological impacts of hydrological operations, affecting them at all life stages through three key aspects of Everglades ecology: (1) food webs, (2) diversity and productivity, and (3) freshwater flow. Responses of crocodilians are directly related to suitability of environmental conditions and hydrologic change. Correlations between biological responses and environmental conditions contribute to an understanding of species’ status and trends over time. Positive or negative trends of crocodilian populations relative to hydrologic changes permit assessment of positive or negative trends in restoration.
Invasive species represent a significant threat to global biodiversity and a substantial economic burden. Burmese pythons, giant constricting snakes native to Asia, now are found throughout much of southern Florida, including all of Everglades National Park (ENP). Pythons have increased dramatically in both abundance and geographic range since 2000 and consume a wide variety of mammals and birds. Here we report severe apparent declines in mammal populations that coincide temporally and spatially with the proliferation of pythons in ENP. Before 2000, mammals were encountered frequently during nocturnal road surveys within ENP. In contrast, road surveys totaling 56,971 km from 2003-2011 documented a 99.3% decrease in the frequency of raccoon observations, decreases of 98.9% and 87.5% for opossum and bobcat observations, respectively, and failed to detect rabbits. Road surveys also revealed that these species are more common in areas where pythons have been discovered only recently and are most abundant outside the python's current introduced range. These findings suggest that predation by pythons has resulted in dramatic declines in mammals within ENP and that introduced apex predators, such as giant constrictors, can exert significant top-down pressure on prey populations. Severe declines in easily observed and/or common mammals, such as raccoons and bobcats, bode poorly for species of conservation concern, which often are more difficult to sample and occur at lower densities.
Based on molecular phylogeny of available complete mitochondrial DNA (mtDNA) genome sequences reveals that Crocodylus siamensis and C. porosus are closely related species. Yet, the sequence divergence of their mtDNA showed only a few values under conspecific level. In this study, a new haplotype (haplotype2, EF581859) of the complete mtDNA genome of Siamese crocodile (C. siamensis) was determined. The genome organization, which appeared to be highly similar to haplotype1 (DQ353946) mtDNA genome of C. siamensis, was 16,814 bp in length. However, the sequence divergence between the two genomes differed by around 7-10 and 0.7-2.1% for the haplotype1 between C. siamensis and C. porosus (AJ810453). These results were consistent with the phylogenetic relationship among the three genomes, suggesting that C. siamensis haplotype1 mtDNA genome might be the hybrid or the intraspecific variation of C. porosus. On the other hand, our specimen was found to be a true C. siamensis. Simultaneously, the seven species-specific DNA markers designed based on the distinctive site between haplotype2 mtDNA sequences of C. siamensis and haplotype1 mtDNA sequence of C. siamensis-C. porosus were successfully used to distinguish C. siamensis from C. porosus. These effective markers could be used primarily for rapid and accurate species identification in population, ecology and conservation studies.
Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.
[Extract] Advancements in evolutionary genetics, as well as the conservation of biodiversity, increasingly require direct analyses of sequence variation in nuclear DNA. Recent studies indicate that nuclear introns have variabilities useful for both phylogenetics and population genetics (reviewed in Friesen 2000); however, use of introns is currently limited by the paucity of polymerase chain reaction (PCR) primers that have been demonstrated to have broad taxonomic utility (although several primers with less general or uncertain utilities have been published; reviewed in Friesen 2000). We have designed 30 general PCR primers for nuclear introns for vertebrates.
With millions of species and their life-stage transformations, the animal kingdom provides a challenging target for taxonomy. Recent work has suggested that a DNA-based identification system, founded on the mitochondrial gene, cytochrome c oxidase subunit 1 (COI), can aid the resolution of this diversity. While past work has validated the ability of COI sequences to diagnose species in certain taxonomic groups, the present study extends these analyses across the animal kingdom. The results indicate that sequence divergences at COI regularly enable the discrimination of closely allied species in all animal phyla except the Cnidaria. This success in species diagnosis reflects both the high rates of sequence change at COI in most animal groups and constraints on intraspecific mitochondrial DNA divergence arising, at least in part, through selective sweeps mediated via interactions with the nuclear genome.
Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.
Unlabelled:
RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively.
Availability:
icwww.epfl.ch/~stamatak
The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented.
BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license.
BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.
Etude comparative de 3 methodes de lavage d'estomac chez le caiman pour etudier le regime alimentaire. La methode proposee est celle du tuyau d'arrosage avec des mouvements de Heimlich (hose with Heimlich maneuvers).
Mortality of some species of estuarine fishes and invertebrates along the Georgia coast was associated with the presumably caused by abnormally cold water temperatures in January 1970. Mortality was low in most estuarine species but high in star drum and white shrimp in the Duplin River and Doboy Sound. Affected star drums and silver perches became weakened and lost their equilibrium. Most of these apparently died from suffocation or freezing when they were left stranded in the marsh by receding ebb tides.
We follow a biological invasion model that consists of a series of five consecutive obligatory stages, concluding with stages 4a and 5 (i.e., widespread = invasive species). The State of Florida is infamous for having the most introduced (stages 2-5) amphibians and reptiles in the United States. However, there is disagreement regarding their numbers as well as identification in some cases. Unverified claims of species being introduced (stage 2), or established (stages 3-5) without evidence (i.e., a voucher specimen or photograph) are prevalent in the literature. It is crucial to provide data on all known non-indigenous herpetofaunal species via vouchers to help keep numbers of species consistent, accurately identify species, document when and where a particular species is found, and identify the invasion pathway and current invasion stage of each species. In this study, we use vouchers to confirm interceptions and introductions of all known non-indigenous amphibians and reptiles in Florida from 1863 through 2010, provide a list of these species along with their invasion pathways and current ecological status (i.e., invasion stage), and provide a species account for each newly confirmed species. We include species that were previously reported in the literature but lacking an associated voucherand provide greater details on previously reported species and those species whose invasion stage has been upgraded to established (stages 3-5). Based on nearly two decades of field work along with examination of museum records and literature, we confirm three intercepted and 137 introduced amphibian and reptile taxa in Florida. Of these, 56 are established (i.e., reproducing; stages 3-5), including three frogs, four turtles, one crocodilian, 43 lizards, and five snakes. Of 149 total independent introduction pathways (i.e., including a different pathway one time only for each taxon) for the 140 total non-indigenous taxa above, two (1.34%) are related to the biological control pathway, four (2.68%) to the zoo pathway, 18 (12.08%) to the cargo pathway, and 125 (83.89%) to the pet trade pathway. Florida now ranks as having the largest number of established non-indigenous herpetofaunal species in the entire world. Despite current state laws that make it illegal to release any non-indigenous animal in Florida without first obtaining a permit from the Florida Fish and Wildlife Conservation Commission, enforcement is difficult, and no person has ever been prosecuted for the establishment of a non-indigenous animal species in Florida. Because current state and federal laws have not been effective in curtailing the ever-increasing number of illegal introductions, laws need to be modified and made enforceable. At the very least, those responsible for introductions should be held accountable for compensation to clean up (= extermination) of those species for which they are responsible. Lastly, we strongly support the creation of an Early Detection and Rapid Response program to quickly identify newly found introduced species for eradication attempts. This paper will also serve as a baseline to document future introductions.
Reliable recovery of the 5'''' region of the cytochrome c oxidase 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all fish species. In this study, we develop and test primer cocktails with a view towards increasing the efficiency of barcode recovery. Specifically, we evaluate the success of polymerase chain reaction amplification and the quality of resultant sequences using three primer cocktails on DNA extracts from repre- sentatives of 94 fish families. Our results show that M13-tailed primer cocktails are more effective than conventional degenerate primers, allowing barcode work on taxonomically diverse samples to be carried out in a high-throughput fashion.
ABSTRACT The use of simple terms to articulate ecological concepts can confuse ideological debates and undermine management efforts. This problem is particularly acute in studies of nonindigenous species, which alternatively have been called ‘exotic’, ‘introduced’, ‘invasive’ and ‘naturalised’, among others. Attempts to redefine commonly used terminology have proven difficult because authors are often partial to particular definitions. In an attempt to form a consensus on invasion terminology, we synthesize an invasional framework based on current models that break the invasion process into a series of consecutive, obligatory stages. Unlike previous efforts, we propose a neutral terminology based on this framework. This ‘stage-based’ terminology can be used to supplement terms with ambiguous meanings (e.g. invasive, introduced, naturalized, weedy, etc.), and thereby improve clarity of future studies. This approach is based on the concept of ‘propagule pressure’ and has the additional benefit of identifying factors affecting the success of species at each stage. Under this framework, invasions can be more objectively understood as biogeographical, rather than taxonomic, phenomena; and author preferences in the use of existing terminology can be addressed. An example of this recommended protocol might be: ‘We examined distribution data to contrast the characteristics of invasive species (stages IVa and V) and noninvasive species (stages III and IVb)’.
Relationships of the newly discovered dwarf crocodiles from Mauritania were inferred from mitochondrial 12S sequences. Specimens from 13 different Crocodylus niloticus populations (from East Africa, West Africa and Madagascar) were compared. Additional representatives of the genus Crocodylus (one from Africa and one from Australia), the African genus Osteolaemus and the South American alligatorid Paleosuchus palpebrosus (as outgroup) were included in the analysis. Maximum-likelihood and Bayesian analyses yielded relationships that were strikingly different from currently prevailing phylogenetic hypotheses. Both analyses consistently revealed two groups, one consisting of the monophyletic West- and Central African populations and the other of a paraphyletic group containing the East African and Madagascan populations. High genetic divergence between those groups indicates separation on the species level. Furthermore ‘C’ cataphractus is clearly shown not to be a member of the genus Crocodylus. The resulting nomenclatural changes are discussed. To cite this article: A. Schmitz et al., C. R. Palevol 2 (2003).
Nile crocodiles (Crocodylus niloticus) are one of the few dangerous predators regularly found outside protected wildlife areas. This is particularly so in northeastern Namibia where an extensive network of rivers and wetlands coupled with successful conservation measures has allowed crocodile populations to flourish since uncontrolled exploitation ended over three decades ago. This area is predominantly communal land characterized by numerous subsistence communities dependent on river and wetland resources. In recent years, the combination of a growing human population and resurgent crocodile populations has resulted in considerable conflict between humans and crocodiles. The principle objective of this study was to quantify the impact of crocodiles on rural livelihoods. Data were obtained from existing records and through community surveys on the lower Kavango, Chobe and Kwando rivers and upper Zambezi River. Existing estimates suggest an annual loss of 255 domestic cattle per year for northeastern Namibia whilst community survey estimates suggest a substantially greater annual loss of 6864 cattle per year. Community surveys also revealed conflict between crocodiles and artisinal fishermen, with an estimated 71 500 fishing nets damaged by crocodiles per year. Human-crocodile conflict in Namibia may have greater impacts than previously assumed, and may undermine conservation and development objectives.
When the American Crocodile (Crocodylus acutus) was declared endangered in 1975, scant data were available for making management decisions. Results of intensive studies conducted during the late 1970s and early 1980s by the National Park Service, Florida Game and Fresh Water Fish Commission, and Florida Power and Light Company resulted in an optimistic outlook for crocodiles. However, new issues face crocodiles today. Florida and Biscayne bays have undergone changes that have caused concern for the health of these ecosystems. The purpose of this paper is to review results of monitoring programs for C. acutus that have been used as a basis for consideration of reclassification of this endangered species and for restoration of its endangered ecosystem. More crocodiles and nests occur in more places today than in 1975. The maximum number of nesting females in Florida has increased from 20 in 1975 to 85 in 2004, and the number of concentrations of nesting effort from two to four. This evidence supports the proposed reclassification of the American Crocodile from endangered to threatened. However, crocodiles are still threatened by modification of habitat because of development adjacent to crocodile habitat and will benefit from restored freshwater flow into estuaries. As crocodiles continue to increase in number and expand into new areas, interactions with humans will occur more frequently. The challenge of integrating a recovering population of the American Crocodile with an ever-increasing use of coastal areas by humans will be the final challenge in successful recovery of this once critically endangered species.
(1) In a study of the population ecology of the Nile crocodile at Ngezi, Zimbabwe, animals were measured, and thermal and feeding data collected during a 3-year mark-recapture experiment. (2) Juvenile growth was confined to the hot season and physical condition declined in the cool season. Large animals grew in irregular spurts. (3) Low cool-season growth was attributed to the physiological affects of temperature on feeding. Juvenile body temperatures equilibrated with the water to which they returned at night and were therefore as high as 30 degrees C in the hot season, but fell to 15 degrees C in the cool. Animals of all sizes basked in the sun, but only for short periods in the cool season did body temperatures exceed 25 degrees C and therefore approach temperatures efficient for digestion. Juveniles were more often seen feeding and were more replete in the hot season. Hatchlings were able to grow at lower temperatures than older animals. (4) On the basis of size, it was impossible to assign juveniles to accurate age-classes after 3 years, and growth curves resulting from the estimation of individual ages by skeletochronology were more accurate than those constructed from growth data. (5) Because growth was slow, females took approximately 30 years to reach sexual maturity. The growth rate of males declined more slowly than that of females and thus they attained larger sizes. (6) At a size of 600 mm snout-vent length, the diet of juveniles changed from a predominance of insects to fish and birds and a concurrent reversal of several important allometric relationships of the head was believed to be an adaptation for the efficient capture of prey of an increasing size. A fundamental change of home range behaviour also occurred in these animals and the abruptness of the dietary transition may partly reflect a change in prey availability.
The American crocodile was declared endangered in the United States in 1975. At that time 75% of the remaining crocodile nests
were in Everglades National Park, in Florida Bay. In 1980, the National Park Service established a crocodile sanctuary in
northeastern Florida Bay to protect nesting and nursery habitat. In 1985, a monitoring program, focused on nesting, growth,
and survival, was established to evaluate the effects of modified water deliveries on crocodiles in Florida Bay. The number
and range of crocodile nests increased between 1970 and 1995, but nesting success decreased slightly. Nests on artificial
substrates in the Greater Flamingo-Cape Sable area accounted for most of the increase in nests. Nests on artificial substrates
were more prone to predation by raccoons. At least 1.5% of marked hatchlings survived for more than 12 mo, and growth rates
were variable. Detailed information on growth and survival of crocodiles is still lacking. It is no longer a question of whether
crocodiles with survive in Florida Bay, but how ecosystem restoration and management can be applied to improve conditions
for crocodiles.
Silvopasture, which combines trees, forages, and shrubs with livestock operations, has potential for limiting phosphorus runoff, sequestering atmospheric carbon dioxide, and improving habitat for wildlife. This study estimates the public demand for these environmental services in south-central Florida's Lake Okeechobee watershed using a stated preference approach. The results from a random parameter logit model reveal that households would pay US$30.24–71.17 per year for 5 years for these environmental benefits. These estimates provide a basis for formulating policies to promote silvopasture practices in the Lake Okeechobee watershed.
The Nile crocodile (Crocodylus niloticus) is an ancient icon of both cultural and scientific interest. The species is emblematic of the great civilizations of the Nile River valley and serves as a model for international wildlife conservation. Despite its familiarity, a centuries-long dispute over the taxonomic status of the Nile crocodile remains unresolved. This dispute not only confounds our understanding of the origins and biogeography of the 'true crocodiles' of the crown genus Crocodylus, but also complicates conservation and management of this commercially valuable species. We have taken a total evidence approach involving phylogenetic analysis of mitochondrial and nuclear markers, as well as karyotype analysis of chromosome number and structure, to assess the monophyletic status of the Nile crocodile. Samples were collected from throughout Africa, covering all major bioregions. We also utilized specimens from museum collections, including mummified crocodiles from the ancient Egyptian temples at Thebes and the Grottes de Samoun, to reconstruct the genetic profiles of extirpated populations. Our analyses reveal a cryptic evolutionary lineage within the Nile crocodile that elucidates the biogeographic history of the genus and clarifies long-standing arguments over the species' taxonomic identity and conservation status. An examination of crocodile mummy haplotypes indicates that the cryptic lineage corresponds to an earlier description of C. suchus and suggests that both African Crocodylus lineages historically inhabited the Nile River. Recent survey efforts indicate that C. suchus is declining or extirpated throughout much of its distribution. Without proper recognition of this cryptic species, current sustainable use-based management policies for the Nile crocodile may do more harm than good.
There is a surprising lack of genetic data for the Cuban crocodile (Crocodylus rhombifer), especially given its status as a critically endangered species. Samples from captive individuals were used to genetically characterize this species in comparison with other New World crocodilians. Partial mitochondrial sequence data were generated from cyt-b (843 bp) and the tRNA(Pro)- tRNA(Phe)-D-loop region (442 bp). Phylogenetic analyses were performed by generating maximum parsimony, maximum likelihood, and Bayesian-based topologies. In addition, in an effort to identify species-specific alleles, ten polymorphic microsatellite loci were genotyped. Distance and model-based clustering analyses were performed on microsatellite data, in addition to a model-based assignment of hybrid types. Both mitochondrial and nuclear markers identified two distinct C. rhombifer genetic sub-clades (alpha and beta); and microsatellite analyses revealed that most admixed individuals were F(2) hybrids between C. rhombifer-alpha and the American crocodile (C. acutus). All individuals in the C. rhombifer-beta group were morphologically identified as C. acutus and formed a distinct genetic assemblage. J. Exp. Zool. 309A:649-660, 2008. (c) 2008 Wiley-Liss, Inc.
High-throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require analysis approaches that are more sophisticated, and often very computationally intensive. Thus, making sense of high-throughput data requires informatics support. Galaxy (http://galaxyproject.org) is a software system that provides this support through a framework that gives experimentalists simple interfaces to powerful tools, while automatically managing the computational details. Galaxy is distributed both as a publicly available Web service, which provides tools for the analysis of genomic, comparative genomic, and functional genomic data, or a downloadable package that can be deployed in individual laboratories. Either way, it allows experimentalists without informatics or programming expertise to perform complex large-scale analysis with just a Web browser.
The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/.