Draft assembly and annotation of the Cuban crocodile (Crocodylus rhombifer) genome.

OBJECTIVES: The new data provide an important genomic resource for the Critically Endangered Cuban crocodile (Crocodylus rhombifer). Cuban crocodiles are restricted to the Zapata Swamp in southern Matanzas Province, Cuba, and readily hybridize with the widespread American crocodile (Crocodylus acutus) in areas of sympatry. The reported de novo assembly will contribute to studies of crocodylian evolutionary history and provide a resource for informing Cuban crocodile conservation. DATA DESCRIPTION: The final 2.2 Gb draft genome for C. rhombifer consists of 41,387 scaffolds (contigs: N50 = 104.67 Kb; scaffold: N50-518.55 Kb). Benchmarking Universal Single-Copy Orthologs (BUSCO) identified 92.3% of the 3,354 genes in the vertebrata_odb10 database. Approximately 42% of the genome (960Mbp) comprises repeat elements. We predicted 30,138 unique protein-coding sequences (17,737 unique genes) in the genome assembly. Functional annotation found the top Gene Ontology annotations for Biological Processes, Molecular Function, and Cellular Component were regulation, protein, and intracellular, respectively. This assembly will support future macroevolutionary, conservation, and molecular studies of the Cuban crocodile.

PAHs in franciscana dolphins from the Southwestern Atlantic Ocean: Concentration and maternal transfer assessments.

Polycyclic aromatic hydrocarbons (PAHs) are organic compounds ubiquitous in the environment and known for their toxic, mutagenic, and carcinogenic effects. These compounds can bioaccumulate in the biota and be transferred through trophic webs. The franciscana dolphin (Pontoporia blainvillei), as top predators, can be an environmental sentinels. Thus, this study aimed to provide data about PAHs concentration in their hepatic tissue collected on the coast of Espírito Santo (Franciscana Management Area, FMA Ia), Rio de Janeiro (FMA IIa), and São Paulo states (FMA IIb), in Southeastern Brazil. PAHs were detected in 86 % of franciscana dolphins (n = 50). The highest ∑PAHsTotal median concentration was reported in FMA Ia followed by FMA IIb and FMA IIa (1055.6; 523.9, and 72.1 ng.g-1 lipid weight, respectively). Phenanthrene was detected in one fetus and two neonates, showing maternal transfer of PAHs in these dolphins. Evaluating PAHs with potential toxic effects is of utmost importance for the conservation of a threatened species.

Ten years from propagule to mature plant of Butia purpurascens Glassman (Arecaceae): an endemic and endangered palm of the Brazilian Cerrado / Dez anos entre o propágulo e a planta madura de Butia purpurascens Glassman (Arecaceae): uma palmeira endêmica e ameaçada de extinção do Cerrado brasileiro

With occurrence mainly in the southwest Goiás, Butia purpurascens has fruits and leaves widely extracted by the regional population. Coexists with exotic grasses, frequent burnings and cattle's grazing and trampling. Young individuals are rarely seen. We aim to provide information about propagules, seedling formation and the monitoring of saplings of B. purpurascens until adults in reproductive phase. Fruits were selected, measured and benefited after harvest. Of 6,000 fruits collected 3,112 were discarded for being perforated by Conotrachelus weevils. The experiment divided 2,600 fruits into 13 treatments, distributed in ripe and immature fruits, with and without pulp. In addition, we adopt mechanical and chemical break dormancy mechanisms, different storage periods and seeding depths. After sixteen months of monitoring, the formation of eleven seedlings was obtained without distinction of any treatment. Seedlings and saplings developed slowly, taking two years to emit the first metaphyll. Over time, ten individuals died, most from fungal attack. After ten years, the only surviving palm generated two inflorescences, which produced fruit. The inefficient seedling production and the slow development of saplings, combined with the impact of the extractivism and the high rate of predation of the pyrenes, suggest the low recruitment rate of the species observed, in natural conditions. This type of data is one of the important tools for creating guidelines for the species conservation. Therefore, we suggest considering the reclassification of B. purpurascens as a Critically Endangered species in the Official List of Threatened Brazilian Species of Extinction.

Com ocorrência concentrada no sudoeste goiano, Butia purpurascens tem frutos e folhas amplamente extraídos pela população regional. Coexiste com gramíneas exóticas, queimadas frequentes, além do pastejo e pisoteamento por gado. Os indivíduos jovens raramente são vistos. Este trabalho teve como objetivo fornecer informações sobre propágulos, formação de plântulas e monitoramento de indivíduos jovens de B. purpurascens até adultos em fase reprodutiva. Os frutos foram selecionados, medidos e beneficiados após a colheita. Dos 6.000 frutos coletados, 3.112 foram descartados por estarem perfurados por gorgulhos do gênero Conotrachelus. O experimento dividiu 2.600 frutos em 13 tratamentos, distribuídos em frutos maduros e imaturos, com polpa e despolpados. Além da adoção de mecanismos mecânicos e químicos de quebra de dormência, períodos de armazenamento e profundidades de plantio diferentes. Após 16 meses de monitoramento, a formação de 11 plântulas foi obtida sem distinção de qualquer tratamento. Plântulas e indivíduos jovens se desenvolveram lentamente, levando dois anos para emitir o primeiro metáfilo. Ao longo do tempo, dez indivíduos morreram, a maioria, por ataque fúngico. Após dez anos, a única planta sobrevivente gerou duas inflorescências, as quais produziram frutos. A capacidade de produção de plântulas ineficiente e o lento desenvolvimento das mudas, combinados com o impacto do extrativismo e a alta taxa de predação dos pirênios, sugerem a baixa taxa de recrutamento da espécie observada, em condições naturais. Esse tipo de dado é uma das ferramentas importantes para a criação de diretrizes para a conservação de espécies. Portanto, sugerimos considerar a reclassificação de B. purpurascens como espécie Criticamente Ameaçada na Lista Nacional Oficial de Espécies da Flora Brasileira Ameaçadas de Extinção.

Ten years from propagule to mature plant of Butia purpurascens Glassman (Arecaceae): an endemic and endangered palm of the Brazilian Cerrado

Abstract With occurrence mainly in the southwest Goiás, Butia purpurascens has fruits and leaves widely extracted by the regional population. Coexists with exotic grasses, frequent burnings and cattles grazing and trampling. Young individuals are rarely seen. We aim to provide information about propagules, seedling formation and the monitoring of saplings of B. purpurascens until adults in reproductive phase. Fruits were selected, measured and benefited after harvest. Of 6,000 fruits collected 3,112 were discarded for being perforated by Conotrachelus weevils. The experiment divided 2,600 fruits into 13 treatments, distributed in ripe and immature fruits, with and without pulp. In addition, we adopt mechanical and chemical break dormancy mechanisms, different storage periods and seeding depths. After sixteen months of monitoring, the formation of eleven seedlings was obtained without distinction of any treatment. Seedlings and saplings developed slowly, taking two years to emit the first metaphyll. Over time, ten individuals died, most from fungal attack. After ten years, the only surviving palm generated two inflorescences, which produced fruit. The inefficient seedling production and the slow development of saplings, combined with the impact of the extractivism and the high rate of predation of the pyrenes, suggest the low recruitment rate of the species observed, in natural conditions. This type of data is one of the important tools for creating guidelines for the species conservation. Therefore, we suggest considering the reclassification of B. purpurascens as a Critically Endangered species in the Official List of Threatened Brazilian Species of Extinction.

Resumo Com ocorrência concentrada no sudoeste goiano, Butia purpurascens tem frutos e folhas amplamente extraídos pela população regional. Coexiste com gramíneas exóticas, queimadas frequentes, além do pastejo e pisoteamento por gado. Os indivíduos jovens raramente são vistos. Este trabalho teve como objetivo fornecer informações sobre propágulos, formação de plântulas e monitoramento de indivíduos jovens de B. purpurascens até adultos em fase reprodutiva. Os frutos foram selecionados, medidos e beneficiados após a colheita. Dos 6.000 frutos coletados, 3.112 foram descartados por estarem perfurados por gorgulhos do gênero Conotrachelus. O experimento dividiu 2.600 frutos em 13 tratamentos, distribuídos em frutos maduros e imaturos, com polpa e despolpados. Além da adoção de mecanismos mecânicos e químicos de quebra de dormência, períodos de armazenamento e profundidades de plantio diferentes. Após 16 meses de monitoramento, a formação de 11 plântulas foi obtida sem distinção de qualquer tratamento. Plântulas e indivíduos jovens se desenvolveram lentamente, levando dois anos para emitir o primeiro metáfilo. Ao longo do tempo, dez indivíduos morreram, a maioria, por ataque fúngico. Após dez anos, a única planta sobrevivente gerou duas inflorescências, as quais produziram frutos. A capacidade de produção de plântulas ineficiente e o lento desenvolvimento das mudas, combinados com o impacto do extrativismo e a alta taxa de predação dos pirênios, sugerem a baixa taxa de recrutamento da espécie observada, em condições naturais. Esse tipo de dado é uma das ferramentas importantes para a criação de diretrizes para a conservação de espécies. Portanto, sugerimos considerar a reclassificação de B. purpurascens como espécie Criticamente Ameaçada na Lista Nacional Oficial de Espécies da Flora Brasileira Ameaçadas de Extinção.

Ten years from propagule to mature plant of Butia purpurascens Glassman (Arecaceae): an endemic and endangered palm of the Brazilian Cerrado / Dez anos entre o propágulo e a planta madura de Butia purpurascens Glassman (Arecaceae): uma palmeira endêmica e ameaçada de extinção do Cerrado brasileiro

With occurrence mainly in the southwest Goiás, Butia purpurascens has fruits and leaves widely extracted by the regional population. Coexists with exotic grasses, frequent burnings and cattle's grazing and trampling. Young individuals are rarely seen. We aim to provide information about propagules, seedling formation and the monitoring of saplings of B. purpurascens until adults in reproductive phase. Fruits were selected, measured and benefited after harvest. Of 6,000 fruits collected 3,112 were discarded for being perforated by Conotrachelus weevils. The experiment divided 2,600 fruits into 13 treatments, distributed in ripe and immature fruits, with and without pulp. In addition, we adopt mechanical and chemical break dormancy mechanisms, different storage periods and seeding depths. After sixteen months of monitoring, the formation of eleven seedlings was obtained without distinction of any treatment. Seedlings and saplings developed slowly, taking two years to emit the first metaphyll. Over time, ten individuals died, most from fungal attack. After ten years, the only surviving palm generated two inflorescences, which produced fruit. The inefficient seedling production and the slow development of saplings, combined with the impact of the extractivism and the high rate of predation of the pyrenes, suggest the low recruitment rate of the species observed, in natural conditions. This type of data is one of the important tools for creating guidelines for the species conservation. Therefore, we suggest considering the reclassification of B. purpurascens as a Critically Endangered species in the Official List of Threatened Brazilian Species of Extinction.(AU)

Com ocorrência concentrada no sudoeste goiano, Butia purpurascens tem frutos e folhas amplamente extraídos pela população regional. Coexiste com gramíneas exóticas, queimadas frequentes, além do pastejo e pisoteamento por gado. Os indivíduos jovens raramente são vistos. Este trabalho teve como objetivo fornecer informações sobre propágulos, formação de plântulas e monitoramento de indivíduos jovens de B. purpurascens até adultos em fase reprodutiva. Os frutos foram selecionados, medidos e beneficiados após a colheita. Dos 6.000 frutos coletados, 3.112 foram descartados por estarem perfurados por gorgulhos do gênero Conotrachelus. O experimento dividiu 2.600 frutos em 13 tratamentos, distribuídos em frutos maduros e imaturos, com polpa e despolpados. Além da adoção de mecanismos mecânicos e químicos de quebra de dormência, períodos de armazenamento e profundidades de plantio diferentes. Após 16 meses de monitoramento, a formação de 11 plântulas foi obtida sem distinção de qualquer tratamento. Plântulas e indivíduos jovens se desenvolveram lentamente, levando dois anos para emitir o primeiro metáfilo. Ao longo do tempo, dez indivíduos morreram, a maioria, por ataque fúngico. Após dez anos, a única planta sobrevivente gerou duas inflorescências, as quais produziram frutos. A capacidade de produção de plântulas ineficiente e o lento desenvolvimento das mudas, combinados com o impacto do extrativismo e a alta taxa de predação dos pirênios, sugerem a baixa taxa de recrutamento da espécie observada, em condições naturais. Esse tipo de dado é uma das ferramentas importantes para a criação de diretrizes para a conservação de espécies. Portanto, sugerimos considerar a reclassificação de B. purpurascens como espécie Criticamente Ameaçada na Lista Nacional Oficial de Espécies da Flora Brasileira Ameaçadas de Extinção.(AU)

Ten years from propagule to mature plant of Butia purpurascens Glassman (Arecaceae): an endemic and endangered palm of the Brazilian Cerrado / Dez anos entre o propágulo e a planta madura de Butia purpurascens Glassman (Arecaceae): uma palmeira endêmica e ameaçada de extinção do Cerrado brasileiro

With occurrence mainly in the southwest Goiás, Butia purpurascens has fruits and leaves widely extracted by the regional population. Coexists with exotic grasses, frequent burnings and cattle's grazing and trampling. Young individuals are rarely seen. We aim to provide information about propagules, seedling formation and the monitoring of saplings of B. purpurascens until adults in reproductive phase. Fruits were selected, measured and benefited after harvest. Of 6,000 fruits collected 3,112 were discarded for being perforated by Conotrachelus weevils. The experiment divided 2,600 fruits into 13 treatments, distributed in ripe and immature fruits, with and without pulp. In addition, we adopt mechanical and chemical break dormancy mechanisms, different storage periods and seeding depths. After sixteen months of monitoring, the formation of eleven seedlings was obtained without distinction of any treatment. Seedlings and saplings developed slowly, taking two years to emit the first metaphyll. Over time, ten individuals died, most from fungal attack. After ten years, the only surviving palm generated two inflorescences, which produced fruit. The inefficient seedling production and the slow development of saplings, combined with the impact of the extractivism and the high rate of predation of the pyrenes, suggest the low recruitment rate of the species observed, in natural conditions. This type of data is one of the important tools for creating guidelines for the species conservation. Therefore, we suggest considering the reclassification of B. purpurascens as a Critically Endangered species in the Official List of Threatened Brazilian Species of Extinction.

Com ocorrência concentrada no sudoeste goiano, Butia purpurascens tem frutos e folhas amplamente extraídos pela população regional. Coexiste com gramíneas exóticas, queimadas frequentes, além do pastejo e pisoteamento por gado. Os indivíduos jovens raramente são vistos. Este trabalho teve como objetivo fornecer informações sobre propágulos, formação de plântulas e monitoramento de indivíduos jovens de B. purpurascens até adultos em fase reprodutiva. Os frutos foram selecionados, medidos e beneficiados após a colheita. Dos 6.000 frutos coletados, 3.112 foram descartados por estarem perfurados por gorgulhos do gênero Conotrachelus. O experimento dividiu 2.600 frutos em 13 tratamentos, distribuídos em frutos maduros e imaturos, com polpa e despolpados. Além da adoção de mecanismos mecânicos e químicos de quebra de dormência, períodos de armazenamento e profundidades de plantio diferentes. Após 16 meses de monitoramento, a formação de 11 plântulas foi obtida sem distinção de qualquer tratamento. Plântulas e indivíduos jovens se desenvolveram lentamente, levando dois anos para emitir o primeiro metáfilo. Ao longo do tempo, dez indivíduos morreram, a maioria, por ataque fúngico. Após dez anos, a única planta sobrevivente gerou duas inflorescências, as quais produziram frutos. A capacidade de produção de plântulas ineficiente e o lento desenvolvimento das mudas, combinados com o impacto do extrativismo e a alta taxa de predação dos pirênios, sugerem a baixa taxa de recrutamento da espécie observada, em condições naturais. Esse tipo de dado é uma das ferramentas importantes para a criação de diretrizes para a conservação de espécies. Portanto, sugerimos considerar a reclassificação de B. purpurascens como espécie Criticamente Ameaçada na Lista Nacional Oficial de Espécies da Flora Brasileira Ameaçadas de Extinção.

Recovered after an extreme bottleneck and saved by ex situ management: Lessons from the Alagoas curassow (Pauxi mitu [Linnaeus, 1766]; Aves, Galliformes, Cracidae).

A pivotal debate on biodiversity conservation is whether the scarce budgets must be invested in critically endangered taxa or in those with higher chances to survive due to larger population sizes. Addressing the fate of extremely bottlenecked taxa is an ideal way to test this idea, but empirical cases are surprisingly limited. The reintroduction of the extinct-in-the-wild Alagoas curassow (Pauxi mitu) by Brazilian scientists in September 2019 added to the two other known cases of survival to bottlenecks of only two or three individuals. We exploit the reasons why this species has survived, and we report how investments to rescue the Alagoas curassow resulted in the protection of many other taxa, suggesting that in the face of the dramatic number of extinctions expected for the Anthropocene, integration must prevail over a choice.

Determination of chloroplast genome sequence of Magnolia ofeliae A. Vázquez & Cuevas (Magnoliaceae), an endangered Mexican Magnolia.

Magnolia ofeliae A. Vázquez & Cuevas, a plant species endemic to south Jalisco, Mexico, is a critically endangered (CR) species based on the IUCN Red List. In this study, we assembled its complete chloroplast (cp) genome. The total genome size of M. ofeliae was 159,839 bp including four subregions: a large single-copy (LSC) region of 88,027 bp and a small single-copy (SSC) region of 18,752 bp separated by a pair of identical inverted repeat regions (IRs) of 26,530 bp each. The GC content of the cp genome of M. ofeliae is 39.3%. The cp genome encoded a set of 113 genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis results that M. ofeliae is a sister to all other magnolias in the subfamily Magnolioideae.

Inducción de organogénesis in vitro con 6-bencilaminopurina en Cattleya trianae Linden & Rchb.f / Induction of organogenesis in vitro with 6-benzylaminopurine in Cattleya trianae Linden & Rchb.f

RESUMEN La orquídea Cattleya trianae Linden & Rchb.f. es reconocida como flor nacional de Colombia y se encuentra en peligro crítico, al presentar una reducción estimada mayor al 80% en los últimos 100 años, debido a la disminución en la calidad del hábitat y niveles altos de explotación o recolección. La familia Orchidaceae es una de las que mayor número de especies posee en el reino Plantae, con aproximadamente 900 géneros, de los cuales, el 38% es endémico de Colombia, concentrado en la región Andina, con 87,2%. Esta investigación buscó profundizar en el tema de la propagación como mecanismo de conservación, para lo cual, se determinó el efecto de la 6-Bencilaminopurina (6-BAP), sobre el desarrollo in vitro, en Fusagasugá (Cundinamarca), en un diseño de bloques completamente al azar, con 3 repeticiones. Cuerpos protocórmicos provenientes de semillas recolectadas en Pacho (Cundinamarca) fueron sembrados en medio básico Murashige & Skoog, enriquecido con 4 concentraciones de 6-BAP. Los resultados mostraron respuestas diferenciales a la adición de la citoquinina, ya que, con la concentración más alta, se obtuvo el mayor porcentaje de callos, con la de 0,05mg.L-1, el mayor porcentaje de brotes y sin la aplicación del regulador de crecimiento, el mayor porcentaje de raíz.

ABSTRACT The orchid Cattleya trianae Linden & Rchb.f. is recognized as the national flower of Colombia, the species is in a critical danger, presenting an estimated reduction of more than 80% in the last 100 years due to the decrease in habitat quality and high levels of exploitation or harvesting. The Orchidaceae family is one of the largest number of species in the Plant Kingdom, with approximately 900 genera, of which 38% are endemic in Colombia, concentrated in the Andean region with 87.2%. This research sought to deepen in the topic of the propagation as mechanism of protection for their conservation, for which the effect of cytokinin 6-benzylaminopurine (6-BAP) on development was determined in vitro in Fusagasugá (Cundinamarca), in a completely randomized block design with 3 replicates. The protocorm-like bodies from seeds collected in Pacho (Cundinamarca) were sown in a basic medium Murashige and Skoog enriched with 4 concentrations of 6-BAP. The results showed differential responses to the addition of cytokinin, as the highest concentration was obtained the highest percentage of callus, with the 0.05mg. L-1, the highest percentage of shoots and without the application of the growth regulator, the highest root percentage.

Skin lipoma in an Arabian leopard (Panthera paradus nimr)

Background: The Arabian leopard (Panthera paradus nimr) is the largest living felid in the arid Arabian Peninsula and classified on the IUCN red list as critically endangered. Unlike felids, neoplasia prevalence in canids such as benign lipoma and malignant liposarcoma has been long and well documented. Only until recently a plethora of reports emerged demonstrating that neoplasia occurrence in wild exotic felids is prevailed more than expected. Soft tissue tumors arise from fatty cells form either a benign lipoma or a dangerously malignant liposarcoma. Alarming though, such cellular transformation might endanger the life of an already endangered animal. Case: An intact Arabian male leopard living in captivity at the Oman wildlife animal breeding center (N23.70 E58.09 A5.80 m) aged approximately 18 years and weight 31 kg was admitted to the veterinary clinic for semen collection and routine physical examination. The animal was identified with two large adjacent subcutaneous masses on the upper rear left limb, clinically resembling that of a lipomatosis. Only one large tissue mass was surgically excised from the base with no incident of bleeding. Gross examination revealed a soft, smooth, rubbery, homogeneous, lack of internal fluid and whitish color lobule. Morphometry measurement of the mass shows that the weight, diameter, circumference, thickness and surface area were 3.6 gm...

Skin lipoma in an Arabian leopard (Panthera paradus nimr)

Background: The Arabian leopard (Panthera paradus nimr) is the largest living felid in the arid Arabian Peninsula and classified on the IUCN red list as critically endangered. Unlike felids, neoplasia prevalence in canids such as benign lipoma and malignant liposarcoma has been long and well documented. Only until recently a plethora of reports emerged demonstrating that neoplasia occurrence in wild exotic felids is prevailed more than expected. Soft tissue tumors arise from fatty cells form either a benign lipoma or a dangerously malignant liposarcoma. Alarming though, such cellular transformation might endanger the life of an already endangered animal. Case: An intact Arabian male leopard living in captivity at the Oman wildlife animal breeding center (N23.70 E58.09 A5.80 m) aged approximately 18 years and weight 31 kg was admitted to the veterinary clinic for semen collection and routine physical examination. The animal was identified with two large adjacent subcutaneous masses on the upper rear left limb, clinically resembling that of a lipomatosis. Only one large tissue mass was surgically excised from the base with no incident of bleeding. Gross examination revealed a soft, smooth, rubbery, homogeneous, lack of internal fluid and whitish color lobule. Morphometry measurement of the mass shows that the weight, diameter, circumference, thickness and surface area were 3.6 gm...(AU)