A Taxonomic Revision of the Genus Dracophyllum Labill. (Ericaceae)

<p>In recent years the New Zealand biogeographic paradigm has shifted from 'Moa's Ark' (Bellamy et al. 1990) to the view that most biota has dispersed here in the lastà à ± 10 My (Fleming 1975, Pole 1994, McGlone et al. 2001). Large and widely distributed genera on island archipelagos and oceanic islands are important elements for the investigation of evolutionary processes such as dispersal from continents to islands and back, adaptive radiation and in some cases extinction. The genus Dracophyllum (Ericaceae: Richeeae) occurs on the Australian continent and the New Zealand archipelago as well as on many oceanic islands in the region. With its wide distribution, ecological importance and apparent taxonomic complexity, a monograph and phylogenetic study of Dracophyllum will make a valuable contribution towards the understanding of the above- mentioned processes. There is still uncertainty about generic limits within tribe Richeeae (Dracophyllum Labill., Richea R. Br. and Sphenotoma R. Br. ex Sweet). Sphenotoma is geographically isolated (southwest Western Australia), monophyletic and forms a distinct evolutionary lineage that diverged early from Dracophyllum and Richea (Powell et al. 1996, Kron et al. 2002). The generic limits between Dracophyllum and Richea still need to be addressed, preferably by making use of DNA sequence data. There are two fundamental aims of systematics: a) to discover, describe and name all species and b) to document the changes on the branches that have occurred during evolution and to transform these into a predictive classification system that reflects evolution (Systematics 18 Agenda 2000). Systematics is therefore the study of the biological diversity that exists on earth today and its evolutionary history (Judd et al. 1999). Taxonomic revisions, especially of large groups, need to focus on groups that are monophyletic (i.e. comprising an ancestor and all of its descendents) and not constrained by geography. Generic delimitation can become problematic when the flora of a specific region is studied in isolation. Many important aspects of genotypic and phenotypic variation are then not taken into consideration, resulting in a skewed and unrealistic representation of the genus as a whole. The long list of synonyms in the southern hemisphere for the genus Veronica L. is a reflection of this situation: Paederota L., Hebe Comm. ex Juss., Derwentia Raf., Pygmaea Hook.f., Detzneria Schltr. ex Diels, Parahebe W.R.B.Oliv., Chionohebe B.G.Briggs & Ehrend., Leonohebe Heads, Heliohebe Garn.-Jones and Hebejeebie Heads.</p>

A Taxonomic Revision of the Genus Dracophyllum Labill. (Ericaceae)

<p>In recent years the New Zealand biogeographic paradigm has shifted from 'Moa's Ark' (Bellamy et al. 1990) to the view that most biota has dispersed here in the lastà à ± 10 My (Fleming 1975, Pole 1994, McGlone et al. 2001). Large and widely distributed genera on island archipelagos and oceanic islands are important elements for the investigation of evolutionary processes such as dispersal from continents to islands and back, adaptive radiation and in some cases extinction. The genus Dracophyllum (Ericaceae: Richeeae) occurs on the Australian continent and the New Zealand archipelago as well as on many oceanic islands in the region. With its wide distribution, ecological importance and apparent taxonomic complexity, a monograph and phylogenetic study of Dracophyllum will make a valuable contribution towards the understanding of the above- mentioned processes. There is still uncertainty about generic limits within tribe Richeeae (Dracophyllum Labill., Richea R. Br. and Sphenotoma R. Br. ex Sweet). Sphenotoma is geographically isolated (southwest Western Australia), monophyletic and forms a distinct evolutionary lineage that diverged early from Dracophyllum and Richea (Powell et al. 1996, Kron et al. 2002). The generic limits between Dracophyllum and Richea still need to be addressed, preferably by making use of DNA sequence data. There are two fundamental aims of systematics: a) to discover, describe and name all species and b) to document the changes on the branches that have occurred during evolution and to transform these into a predictive classification system that reflects evolution (Systematics 18 Agenda 2000). Systematics is therefore the study of the biological diversity that exists on earth today and its evolutionary history (Judd et al. 1999). Taxonomic revisions, especially of large groups, need to focus on groups that are monophyletic (i.e. comprising an ancestor and all of its descendents) and not constrained by geography. Generic delimitation can become problematic when the flora of a specific region is studied in isolation. Many important aspects of genotypic and phenotypic variation are then not taken into consideration, resulting in a skewed and unrealistic representation of the genus as a whole. The long list of synonyms in the southern hemisphere for the genus Veronica L. is a reflection of this situation: Paederota L., Hebe Comm. ex Juss., Derwentia Raf., Pygmaea Hook.f., Detzneria Schltr. ex Diels, Parahebe W.R.B.Oliv., Chionohebe B.G.Briggs & Ehrend., Leonohebe Heads, Heliohebe Garn.-Jones and Hebejeebie Heads.</p>

Zobellia barbeyronii sp. nov., a New Member of the Family Flavobacteriaceae, Isolated from Seaweed, and Emended Description of the Species Z. amurskyensis, Z. laminariae, Z. russellii and Z. uliginosa

Six Gram-stain-negative, aerobic, rod-shaped, and motile by gliding bacterial strains were isolated from Pacific green and red algae. Phylogenetic analysis based on 16S rRNA gene sequences placed the novel strains into the genus Zobellia as a distinct evolutionary lineage close to Zobellia nedashkovskayae Asnod2-B07-BT and Zobellia laminariae KMM 3676T sharing the highest similarity of 99.7% and 99.5%, respectively. The average nucleotide identity and the average amino acid identity values between strains 36-CHABK-3-33T and Z. nedashkovskayae Asnod2-B07-BT and Z. laminariae KMM 3676T were 89.7%/92.9% and 94.2%/95.8%, respectively. The digital DNA–DNA hybridization values based on the draft genomes between strains 36-CHABK-3-33T and Z. nedashovskayae Asnod2-B07-BT and Z. laminariae KMM 3676T were 39.5 ± 2.5% and 59.6 ± 2.7%, respectively. Multilocus sequence analysis based on house-keeping genes (dnaK, gyrB, pyrH, recA and topA) assigned the alga-associated isolates to the same species, which clustered separately from the recognized species of the genus Zobellia. The strains under study grew at 4–32 °C and with 0.5–8% NaCl and decomposed aesculin, gelatin, DNA, and Tweens 20 and 80, and weakly agar. The DNA G+C content was 36.7% calculated from genome sequence analysis for the strain 36-CHABK-3-33T. The predominant fatty acids of strain 36-CHABK-3-33T (> 5% of the total fatty acids) were iso-C17:0 3-OH, summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH fatty acids), iso-C15:0, iso-C15:1 G, and C15:0. The major polar lipids were phosphatidylethanolamine, three unidentified lipids, and two unidentified aminolipids. The only detected respiratory quinone was MK-6. The significant molecular distinctiveness between the novel isolates and their nearest neighbor was strongly supported by differences in physiological and biochemical tests. Therefore, the six novel strains represent a novel species of the genus Zobellia, for which the name Zobellia barbeyronii sp. nov. is proposed. The type strain is 36-CHABK-3-33T (= KACC 21790T = KMM 6746T).

Spiranthes bightensis (Orchidaceae), a New and Rare Cryptic Hybrid Species Endemic to the U. S. Mid-Atlantic Coast

Recognizing species diversity is challenging in genera that display interspecific similarity and intraspecific variation; hybridization and the evolution of cryptic hybrid species amplifies these challenges. Recent molecular and morphological research focused on the systematics of Spiranthes (Orchidaceae) support hybrid speciation as an important driver of species diversity, particularly within the S. cernua species complex. Working under an integrated history-bound phylogenetic species concept, new molecular and morphometric data provide evidence for a new and rare cryptic hybrid species resulting from the ancient hybridization of S. cernua × S. odorata, here described as S. bightensis. Although S. bightensis is regionally sympatric with S. cernua it does not co-occur with that species, and it is allopatric with respect to S. odorata. Endemic to a narrow region extending from the Delmarva Peninsula to Long Island, New York, this new species occurs in the shadow of the Northeast megalopolis and appears to have undergone a major population decline over the last 200 years. By recognizing this distinct evolutionary lineage as a new species, this research is the first step towards developing conservation protocols for this rare species and highlights the importance of the North American Geologic Coastal Plain for biodiversity conservation and evolution.

Genomic and acoustic differences separate Lilian’s Meadowlark (Sturnella magna lilianae) from Eastern (S. magna) and Western (S. neglecta) meadowlarks

Examining differences among recently diverged populations can provide insight into the traits and evolutionary mechanisms that drive or maintain divergence. The genus Sturnella includes 2 recently diverged species, Sturnella magna (Eastern Meadowlark) and S. neglecta (Western Meadowlark), the former of which has a complex of subspecies distributed across the Americas. Of the S. magna subspecies that occur in the United States, S. m. lilianae is the only one with a disjunct range, occurring in the southwestern United States and central Mexico. It also has markedly different song patterns than all other S. magna subspecies. In order to assess population differentiation, we performed whole-genome sequencing of 35 birds and analyzed song characteristics from 85 birds. Songs from each species and S. m. lilianae were diagnosable using linear discriminant function analysis and support divergence in song between all taxa. Phylogenetic analysis and admixture proportions support 3 distinct clades within North American meadowlarks, and tests of introgression failed to detect a significant signal. Overall, our results indicate that S. m. lilianae exhibits high levels of genetic and vocal differentiation from both S. magna and S. neglecta, with no evidence of introgression between any group, and forms a distinct evolutionary lineage. We thus recommend the elevation of S. m. lilianae to species status.

The unusual biology of marine file snakes with a perspective for the conservation of Acrochordus granulatus

Biodiversity and the function of tropical shallow-water marine environments are threatened by numerous anthropogenic factors, especially climate change, overharvesting of resources, and destruction of habitat. Marine snakes are important components of coastal shallow-water systems and should be considered as indicators of the health of coastal ecosystems such as mangroves. Acrochordid snakes (Acrochordidae: Acrochordus) represent a highly distinct evolutionary lineage with unusual adaptations to shallow water habitats and importance to biodiversity of tropical coastal regions. One of three congeneric species, Acrochordus granulatus (file snake), is an interesting and common inhabitant of coastal estuaries and mangroves in the Philippines. This paper reviews unusual attributes of A. granulatus and provides a perspective for its conservation in coastal habitats. Morphological, physiological, and behavioral characters of this snake are specialized for life in shallow-water marine environments such as mangroves. Unusual and specialized features confer abilities for prolonged submergence and include low metabolic rate, large capacity for oxygen storage, cutaneous gas exchange, nearly complete utilization of oxygen stores during aerobic submergence, intracardiac and cutaneous shunts for regulating blood flow, and reclusive behavior. Fresh water is required for water balance, and file snakes are dependent on rainfall in many habitats where they drink from freshwater lenses formed by precipitation on the surfaces of marine water. File snakes feed largely on fishes and are candidates as bio-indicators of the health of shallow-water coastal habitats. Attention should be given to threatening insults on coastal environments including climate change, habitat destruction, harvesting of resources, and other factors in need of research, monitoring, and plans for abatement. Importantly, conservation can be promoted by educating people about the docile behavior, unusual traits, and interesting ecology of A. granulatus. KEYWORDS: mangrove, shallow water, Acrochordidae, little file snake, conservation physiology, ecophysiology

Genome-Wide SNPs Redefines Species Boundaries and Conservation Units in the Freshwater Mussel Genus Cyprogenia of North America

Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide ddRAD-Seq data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric clusters of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean FST = 0.120) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using SNP data supported results from phylogenetic analyses, which favors recognizing three species of Cyprogenia over the currently recognized two species.A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

Resolving the systematics of Richtersiidae by multilocus phylogeny and an integrative redescription of the nominal species for the genus Crenubiotus (Tardigrada)

The family Richtersiidae, although established recently with the use of phylogenetic methods, was considered potentially paraphyletic at the time of its erection. Until now, the family comprised four genera, Richtersius, Diaforobiotus, Adorybiotus and a newly erected genus Crenubiotus. However, the genetic characterisation for the latter two genera was very limited or absent. To address concerns about the phylogenetic affinity of these two genera, we present a multilocus phylogeny of the families Richtersiidae and Murrayidae based on four molecular markers (18S rRNA, 28S rRNA, ITS-2 and COI). Our results show a distinct evolutionary lineage composed of Adorybiotus and Crenubiotus, which is sister to Murrayidae. In order to accommodate the phylogenetic and morphological distinctiveness of this lineage, we erect a new family, Adorybiotidae fam. nov. The new taxon differs morphologically from other families in the superfamily Macrobiotoidea by a unique combination of traits: (1) the presence of tubercles/cushions with aggregations of microgranules on their surfaces present on all legs and on the dorso-caudal cuticle, (2) a system of internal septa in claws, and (3) buccal apparatus morphology. Moreover, in order to stabilise the taxonomy and nomenclature in the genus Crenubiotus, we redescribe its type species, Crenubiotus crenulatus, by means of integrative taxonomy and designate a new neotype based on a population from the original terra typica.

New Guinea highland wild dogs are the original New Guinea singing dogs

New Guinea singing dogs (NGSD) are identifiable by their namesake vocalizations, which are unlike any other canid population. Their novel behaviors and potential singular origin during dog domestication make them an attractive, but elusive, subject for evolutionary and conservation study. Although once plentiful on the island of New Guinea (NG), they were presumed to currently exist only in captivity. This conclusion was based on the lack of sightings in the lowlands of the island and the concurrent expansion of European- and Asian-derived dogs. We have analyzed the first nuclear genomes from a canid population discovered during a recent expedition to the highlands of NG. The extreme altitude (>4,000 m) of the highland wild dogs’ (HWD) observed range and confirmed vocalizations indicate their potential to be a wild NGSD population. Comparison of single-nucleotide polymorphism genotypes shows strong similarity between HWD and the homogeneous captive NGSD, with the HWD showing significantly higher genetic diversity. Admixture analyses and estimation of shared haplotypes with phylogenetically diverse populations also indicates the HWD is a novel population within the distinct evolutionary lineage of Oceanic canids. Taken together, these data indicate the HWD possesses a distinct potential to aid in the conservation of NGSD both in the wild and under human care.

Chitinasiproducens palmae gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from leaf tissues of oil palm (Elaeis guineensis Jacq.)

A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23T, was isolated from surface-sterilized leaf tissue of an oil palm grown in Singapore and was investigated by polyphasic taxonomy. Phylogenetic analyses based on 16S rRNA gene sequences and 180 conserved genes in the genome of several members of Burkholderiaceae revealed that strain JS23T formed a distinct evolutionary lineage independent of other taxa within the family Burkholderiaceae . The predominant ubiquinone was Q-8. The primary polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminophospholipid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c /C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c /C18 : 1 ω6c). The size of the genome is 5.36 Mbp with a DNA G+C content of 66.2 mol%. Genomic relatedness measurements such as average nucleotide identity, genome-to-genome distance and digital DNA–DNA hybridization clearly distinguished strain JS23T from the closely related genera Burkholderia , Caballeronia , Mycetohabitans , Mycoavidus , Pandoraea , Paraburkholderia , Robbsia and Trinickia . Furthermore, average amino acid identity values and the percentages of conserved proteins, 56.0–68.4 and 28.2–45.5, respectively, were well below threshold values for genus delineation and supported the assignment of JS23T to a novel genus. On the basis of the phylogenetic, biochemical, chemotaxonomic and phylogenomic evidence, strain JS23T is proposed to represent a novel species of a new genus within the family Burkholderiaceae , for which the name Chitinasiproducens palmae gen. nov., sp. nov., is proposed with the type strain of JS23T (= DSM 27307T=KACC 17592T).