Subspecies Status Research Articles

Genetic Distinctness of Sorex caecutiens hallamontanus (Soricomorpha: Mammalia) from Jeju Island in Korea: Cytochrome Oxidase I and Cytochrome b Sequence Analyses

To examine genetic divergences of two endemic Sorex caecutiens subspecies from Korea (S. c. hallamontanus in Korean Jeju Island and S. c. annexus in the mainland Korean Peninsula), we obtained partial cytochrome oxidase I (COI) sequences (429 bp) and complete cytochrome b sequences (1,140 bp) from the two Korean subspecies, and we compared these sequences to the corresponding sequences of S. caecutiens, obtained from GenBank. We found that Jeju S. c. hallamontanus is one of three clades within S. caecutiens, with an average Jukes-Cantor distance of 1.57% in the COI sequences and the distance of 2.07% and 11 fixed site differences in the cytochrome b sequences, indicating that Jeju S. c. hallamontanus is one endemic subspecies with concordant genetic distinctness, although further analyses with nuclear DNA sequences are necessary to confirm these findings. However, S. c. annexus from the mainland Korean Peninsula was not divergent from S. c. macropygmaeus from northeastern China and adjacent Russia, indicating that S. c. annexus from the mainland Korean Peninsula is another endemic subspecies with only morphological differences, although it is necessary to reexamine the subspecies status of S. c. annexus.

Chromosome rearrangements during domestication of cucumber as revealed by high‐density genetic mapping and draft genome assembly

Cucumber, Cucumis sativus L. is the only taxon with 2n = 2x = 14 chromosomes in the genus Cucumis. It consists of two cross-compatible botanical varieties: the cultivated C. sativus var. sativus and the wild C. sativus var. hardwickii. There is no consensus on the evolutionary relationship between the two taxa. Whole-genome sequencing of the cucumber genome provides a new opportunity to advance our understanding of chromosome evolution and the domestication history of cucumber. In this study, a high-density genetic map for cultivated cucumber was developed that contained 735 marker loci in seven linkage groups spanning 707.8 cM. Integration of genetic and physical maps resulted in a chromosome-level draft genome assembly comprising 193 Mbp, or 53% of the 367 Mbp cucumber genome. Strategically selected markers from the genetic map and draft genome assembly were employed to screen for fosmid clones for use as probes in comparative fluorescence in situ hybridization analysis of pachytene chromosomes to investigate genetic differentiation between wild and cultivated cucumbers. Significant differences in the amount and distribution of heterochromatins, as well as chromosomal rearrangements, were uncovered between the two taxa. In particular, six inversions, five paracentric and one pericentric, were revealed in chromosomes 4, 5 and 7. Comparison of the order of fosmid loci on chromosome 7 of cultivated and wild cucumbers, and the syntenic melon chromosome I suggested that the paracentric inversion in this chromosome occurred during domestication of cucumber. The results support the sub-species status of these two cucumber taxa, and suggest that C. sativus var. hardwickii is the progenitor of cultivated cucumber.

Evidence for persistence and a major range extension of the smooth-coated otter (Lutrogale perspicillata maxwelli; Mustelidae, Carnivora) in Iraq

The species IUCN conservation status of smooth-coated otter (Lutrogale perspicillata) is considered ‘Vulnerable’, due to an inferred future population decline caused by habitat loss and sustained exploitation. The status of the Arabian subspecies (L. p. maxwelli) occurring in the Tigris marshes of Iraq and Iran is uncertain due to political problems and limited access to this border region in recent years. With this study we could confirm the persistence of the smooth-coated otter in the marshlands of southern Iraq by using a mitochondrial marker (cytochrome b). Moreover, a second sample from Kurdistan was also identified to be L. perspicillata. This observation represents a major range extension of more than 500 km for this poorly known species. It is recommended to undertake further surveys of suitable habitat in the Tigris wetlands, as well as in Kurdistan, to obtain additional information on the distribution of smooth-coated otter in Iraq, and implement conservation measures in those areas.

Characterization ofMycobacterium orygisasM. tuberculosisComplex Subspecies

The oryx bacilli are Mycobacterium tuberculosis complex organisms for which phylogenetic position and host range are unsettled. We characterized 22 isolates by molecular methods and propose elevation to subspecies status as M. orygis. M. orygis is a causative agent of tuberculosis in animals and humans from Africa and South Asia.

Morphological convergence and molecular divergence: the taxonomic status of Sceloporus serrifer (squamata, phrynosomatidae) subspecies

Martínez‐Méndez, N., Mejía, O., Rocha‐Gómez, A. & Méndez‐De La Cruz, F. R. (2012) Morphological convergence and molecular divergence: the taxonomic status of Sceloporus serrifer (squamata, phrynosomatidae) subspecies. —Zoologica Scripta, 41, 97–108.The systematics of the subspecies included in Sceloporus serrifer has undergone several taxonomic and nomenclatural rearrangements. This species previously comprised two recognized subspecies, Sceloporus serrifer serrifer and Sceloporus serrifer prezygus, which inhabit contrasting habitats. In this study, we re‐evaluate the taxonomic status of both subspecies using molecular and morphological evidence. Sceloporus serrifer serrifer was recovered as a paraphyletic group, whereas S. s. prezygus was recovered as a polyphyletic group. The molecular results indicate the existence of two independent lineages that diverged at least 1.29 Myr, with the populations currently recognized as S. s. prezygus from the Cuchumatanes Mountains representing a secondary invasion of S. s. serrifer from the lowlands. The lack of meristic differences among the highland populations of different species suggests convergence in similar environments achieved by two different lineages.

Genetic diversity and population structure of North America’s rarest heron, the reddish egret (Egretta rufescens)

The global distribution of the reddish egret is characterized by disjunct colonies occurring from the Pacific side of Northwest Mexico to the Caribbean. We examined distantly isolated colonies of reddish egret to determine global population genetic structure. We used seven polymorphic microsatellites to accomplish five goals: (1) to assess range wide population differentiation among reddish egret (Egretta rufescens) populations, (2) identify extent of gene flow, (3) determine any historical occurrence of bottlenecks, (4) assess genetic differentiation between color morphs, (5) clarify subspecies status of E. r. dickeyi, a completely dark morph population located in and around the Baja California peninsula, Mexico. Genetic differentiation was dramatic (global Fst = 0.161) throughout the reddish egrets range extending from Baja California, Mexico to Great Inagua, Bahamas. Differentiation occurred among three distinct regions (Fst = 0.238) but not among colonies/islands within regions suggesting regional philopatry. Genetic diversity (alleles per locus, and heterozygosity) in Baja California Sur, Mexico and Great Inagua, Bahamas populations is lower than in the Texas/Mexico population due to minimal dispersal between regions and smaller population sizes. Dark and white color morphs when present within the same region showed no differentiation. Patterns of recent population bottlenecks are not evident in each of the three regional populations. With evidence of limited gene flow in addition to low genetic diversity and prospects of habitat loss we recommend that reddish egrets be managed as three distinct or evolutionary significant units.

Lineages differentiation and population structure of the light‐vented bulbul Pycnonotus sinensis in China based on mitochondrial DNA and microsatellite analysis

The light-vented bulbul Pycnonotus sinensis is a small resident passerine that is found widely in central and south China, North Vietnam, and some East Asian islands, including Hainan, Taiwan and the Ryukyu Islands. Its subspecies status has been under considerable debate. A total of 10 subspecies have been proposed, but only 4 are widely recognized, including 1 continental taxon, P. s. sinensis, and 3 insular subspecies: P. s. hainanus, P. s. formosae and P. s. orii. Two mitochondrial DNA genes and 9 microsatellite loci were used to investigate the genetic divergence of this species, to identify the evolutionary status of 2 insular subspecies (P. s. hainanus and P. s. formosae) and to uncover probable historical causes that shaped them. The results reveal that P. s. formosae has diverged significantly from the other 2 subspecies because of a substantial time of isolation for populations on Taiwan Island. There was no significant genetic differentiation between P. s. sinensis and P. s. hainanus. The notable morphological difference in P. s. hainanus might be attributed to a rapid, recent adaptation to the tropical environment of Hainan Island. The low genetic divergence between P. s. sinensis and P. s. hainanus might result from a recent divergence or gene flow between them. Two insular subspecies of light-vented bulbul populations might have diverged recently from their continental relatives through a complex evolution history owing to island isolation, ecological isolation, and possibly even hybridization. Both P. s. hainanus and P. s. formosae should be considered important conservation units because of their morphological and genetic distinctiveness.

Allozyme-Based Phylogeny of North AmericanCallophrys(s. l.) (Lycaenidae)

In allozyme generated trees, test populations of species of the North American Callophrys (sensu lato) (a group of hairstreak/elfin butterflies) clustered within the genera Mitoura, Callophrys, Incisalia, and Loranthomitoura. The pine-feeding species of Incisalia clustered weakly, but separately from non-pine feeding species of Incisalia (Deciduphagus). The trees present dissimilarities from recent taxonomic arrangements of Mitoura species and subspecies. Larval food plants (Calocedrus, Juniperus, and Cupressus), often used for distinguishing Mitoura taxa, do not necessarily follow the pattern of genetic relationships among populations. Mitoura thornei and M. muiri probably deserve no greater than subspecies status under M. loki and M. siva respectively. Mitoura gryneus and M. siva populations, considered conspecific by some workers, do not display a gradual geoclinal blend zone and are probably best considered separate taxa. A putative population of M. gryneus from Arkansas may deserve species status.

Salicaceae detoxification abilities in Florida tiger swallowtail butterflies (Papilio glaucus maynardi Gauthier): Novel ability or Pleistocene holdover?

Abstract Florida populations of the eastern tiger swallowtail butterfly, Papilio glaucus L., have unique morphological features and ecological adaptations that have contributed to their subspecies status (P. g. maynardi Gauthier). We describe geographically unique abilities for detoxification of Carolina willow, Salix caroliniana Michx. (Salicaceae), for several Florida populations of P. g. maynardi. Of all the approximately 570 worldwide species of the Papilionidae, such Salicaceae detoxification abilities exist only in the allopatric North American western and northernmost species (P. rutulus Lucas, P. eurymedon Lucas and P. canadensis Rothschild & Jordan). Females of P. glaucus collected from populations in southeastern USA were examined for oviposition preference in 5‐choice assays, and displayed a low preference for Salicaceae (<5%), but larvae from Florida populations exhibited a high survival (>60%) on these plants. Detoxification abilities have previously shown to be autosomally inherited, and can be transferred via natural or hand‐paired interspecific hybrid introgression. However, these Florida populations are at least 700–1 500 km from the nearest hybrids or the hybrid species, P. appalachiensis Pavulaan & Wright, which possess these detoxification abilities. In any case, the Z ( = X)‐linked oviposition preferences for Salicaceae are lacking in these Florida populations, illustrating genetic independence of oviposition preference determination and larval survival/performance abilities. The origins of detoxification abilities are unlikely to be due to recent climate‐driven introgression, and may represent ancestral trait carry‐overs from interglacial refugium populations of the Pleistocene epoch.

Misconceptions about the taxonomy and distribution of Caiman crocodilus chiapasius and C. crocodilus fuscus (Reptilia: Crocodylia: Alligatoridae)

Four subspecies are currently recognized for the Spectacled Caiman, Caiman crocodilus (Linnaeus 1758): Caiman crocodilus fuscus (Cope 1868: Perosuchus fuscus), described from a single specimen from the Magdalena River, Colombia; C. c. chiapasius (Bocourt 1876: Alligator chiapasius), described from the Tonalá Valley, Chiapas, México; C. c. apaporiensis (Medem 1955) from the upper Apaporis River, Colombia; and, C. c. crocodilus (Linnaeus 1758: Lacerta crocodilus), named for the species originally described (Smith & Smith 1977; Busack & Pandya 2001). Caiman yacare was previously considered to be a fifth subspecies (i.e., C. c. yacare), but it is now generally accepted that it is a full species (King & Burke 1989), and is no longer treated as a subspecies (Velasco & Ayarzagüena 2010). There is some confusion about the current distributions of C. c. chiapasius and C. c. fuscus, and although some works have attempted to clarify this situation (Busack & Pandya 2001), the confusion still remains (i.e., Rueda-Almonacid et al. 2007; Velasco & Ayarzagüena 2010). Here, we present a brief review of the taxonomic status of caiman subspecies, and its implications for their distributions.

A revision of the Thyropygus allevatus group. Part 4: the T. cuisinieri subgroup (Diplopoda: Spirostreptida: Harpagophoridae)

The Thyropygus cuisinieri subgroup of the T. allevatus group is revised. A new species is described from Thailand: T. jarukchusri n. sp. The following species are re-described: T. cuisinieri Carl, 1917, T. carli Attems, 1938, and T. foliaceus (Demange, 1961), new status (elevated from subspecies status under T. cuisinieri).

A revision of the Thyropygus allevatus group. Part 3: the T. induratus subgroup (Diplopoda: Spirostreptida: Harpagophoridae)

The Thyropygus induratus subgroup of the T. allevatus group is revised. Three new species are described from Thailand: T. dormiens n. sp., T. laterolobatus n. sp. and T. macrosiamensis n. sp. The following species are redescribed and re-elevated from subspecies status under T. allevatus (Karsch, 1881): Thyropygus induratus Attems, 1936 (= T. punctatus Attems, 1938, new synonym), Thyropygus quietus Attems, 1938, Thyropygus resimus Attems, 1938, and Thyropygus uncinatus (Demange, 1961). Thyropygus siamensis Verhoeff, 1938 (= Thyropisthus ligulus Demange, 1961, new synonym), is re-described. A case of species with identical gonopods but very different body size (T. induratus and T. quietus) is discussed.

Extreme Color Variation within Populations of the Common Gartersnake, Thamnophis sirtalis, in Central North America, with Implications for Subspecies Status

We report on the remarkable variation and frequency of color morphs within and among eight populations of the Common Gartersnake (Thamnophis sirtalis) in central Manitoba, Canada and one on Isle Royale, Michigan, USA. Five color morph categories are identified, one melanistic and four scored on a qualitative scale based on expression of red pigment. In the most northern population (Jenpeg, 54.464°N, 98.115°W) and two island populations (George Island, Lake Winnipeg, 52.819°N, 97.620°W; Isle Royale, 48.102°N, 88.601°W), all five color morphs were expressed. The northernmost population also exhibited sexual color dimorphism, with female snakes expressing significantly more red than males. In contrast, two central and western populations showed very little variation, with only two of the most similar color morphs present. We provide the first report of erythristic snakes in Manitoba, found in three separate locations around Lake Winnipeg. Melanistic snakes are also reported from three new localities in the province, all widely disjunct from previously identified sites around Lake Winnipegosis. Manitoban and Isle Royale populations are compared with color frequency data from sites in mainland Michigan and in Kansas. Color patterns among populations do not follow traditionally recognized zones of intergradation between T. s. parietalis and T. s. sirtalis. The extreme intrapopulational variation suggests that subspecies of T. sirtalis based on color are of questionable validity.

Southern extension of the geographical range of the pygmy marmoset <i>Cebuella pygmaea niveiventris</i> (Lönnberg, 1940) in the southwestern Amazon basin, state of Rondônia, Brazil

No abstract

Genetic structure and subspecies divergence of Lepus capensis in Xinjiang

To date, the genetic structure and genetic diversity of Lepus capensis in Xinjiang has not been systematically studied at the molecular level, and its subspecies taxonomic status has been under debate for years. According to traditional morphology, there are three subspecies of L. capensis distributed in Xinjiang: L.c. centrasiaticus, L.c. lehmanni and L.c. pamirensis. In this study, we determined 592 bp D-loop sequences of 87 cape hares from Xinjiang Province. Forty-four haplotypes were defined based on 148 polymorphic sites. Both the haplotype diversity (0.977+/-0.005) and nucleotide diversity (0.064+/-0.031) are high. FST P values are significantly high and no haplotype was shared among the four geographic populations, indicating that genetic differentiation among populations is significant. AMOVA shows that most of the genetic differentiation occurred among geographic groups, indicating that geographic isolation such as mountains and deserts might make an effective barrier against gene flow. Both the phylogenetic tree and median-joining network grouped 44 haplotypes into four distinct clades corresponding to four geographic areas, indicating an obvious phylogeographic pattern. Our data supported the subspecies status of L. c. lehmanni. The fact that haplotypes of L. c. centrasiaticus were grouped into two distinct clades suggests that this traditional subspecies should be considered as two subspecies. In addition, L. c. pamirensis shows a significantly higher sequence divergence compared to other subspecies, and the difference even reached the level of species.

Phylogeny, Biodiversity, and Species Limits of Passerine Birds in the Sino-Himalayan Region—A Critical Review

We analyzed passerine biodiversity and phylogeography in the Sino-Himalayan region with respect to neighboring areas, especially the Siberian taiga zone to the north and tropical Asia southeast of the Himalayas and mountainous parts of southwest China. Fresh results, informative about evolutionary processes in that area, were obtained mainly by the application of new methods in passerine systematics, acoustic and molecular genetic markers. It became evident that species with areas in the Himalayas and southwest China and, in addition, often with disjunct areas in Siberia, actually belong to swarms of closely related, mostly allopatric species. In many cases these differ markedly in vocalizations and are deeply split according to molecular genetic markers. External morphology of the constituent taxa quite often remained surprisingly homogeneous and thus resulted in traditional subspecies status of single populations at best. Other such well-differentiated taxa were often overlooked and only discovered by m...

Mitochondrial phylogeny of tamarins (Saguinus, Hoffmannsegg 1807) with taxonomic and biogeographic implications for theS. nigricollisspecies group

Tamarins of the genus Saguinus, subfamily Callitrichinae, represent one of the most diverse primate radiations. So far, about 35 taxa have been described, but detailed information about their taxonomy and phylogeny is still lacking. To further elucidate the phylogenetic relationships and the biogeographic history within the genus, and to contribute to a more reliable classification of its taxa, we sequenced the complete mitochondrial cytochrome b gene and the hypervariable region I of the D-loop. Therefore, we mainly used fecal samples from wild tamarins collected during two expeditions to the Peruvian Amazon, an area of high tamarin diversity. Our data suggest that the numerous taxa of the S. nigricollis species group are derived from a common ancestor that separated from the other representatives of the genus ~10 mya. Most taxa of the S. nigricollis group form monophyletic clusters, which mainly originated in a single rapid radiation ~2.9 mya. S. fuscicollis and S. nigricollis appear as polyphyletic taxa, but we could identify various clusters, which are mainly consistent with differences in coat coloration. We could confirm most of the existing taxa as distinct entities and suggest species status for fuscicollis, illigeri, lagonotus, leucogenys, nigricollis, nigrifrons, tripartitus, and weddelli. Our genetic data do not support a separate status for melanoleucus and graellsi, but due to differences in fur coloration, we give them subspecies status. The species group most likely originated in western Amazonia and diversified during the decline of the Acre wetland and the formation of the Amazonian river system.

Phylogeography and conservation genetics of Lake Qinghai scaleless carp Gymnocypris przewalskii

The objective of this study was to examine the spatial genetic relationships of the Lake Qinghai scaleless carp Gymnocypris przewalskii within the Lake Qinghai system, determining whether genetic evidence supports the current taxonomy of Gymnocypris przewalskii przewalskii and Gymnocypris przewalskii ganzihonensis and whether Gymnocypris przewalskii przewalskii are returning to their natal rivers to spawn. Comparison of mitochondrial (control region) variation (42 haplotypes in 203 fish) of G. przewalskii with the postulated ancestral species found in the Yellow River, Gymnocypris eckloni (10 haplotypes in 23 fish), indicated no haplotype sharing, but incomplete lineage sorting. Consistent with the sub-species status, an AMOVA indicated that the Ganzi River population was significantly different from all other river populations (F(ST) = 0·1671, P < 0·001). No genetic structure was found among the other rivers in the Lake Qinghai catchment. An AMOVA of amplified fragment length polymorphism (AFLP) loci, however, revealed significant genetic differences between most spawning populations (F(ST) = 0·0721, P < 0·001). Both mitochondrial and AFLP data found significant differences among G. p. przewalskii, G. p. ganzihonensis and G. eckloni (F(ST) values of 0·1959 and 0·1431, respectively, P < 0·001). Consistent with the incomplete lineage sorting, Structure analysis of AFLP loci showed evidence of five clusters. One cluster is shared among all sample locations, one is unique to G. p. ganzihonensis and G. eckloni, and the others are mostly found in G. p. przewalskii. Genetic evidence therefore supports the current taxonomy, including the sub-species status of G. p. ganzihonensis, and is consistent with natal homing of most Lake Qinghai populations. These findings have significant implications for the conservation and management of this unique and threatened species. The evidence suggests that G. p. przewalskii should be treated as a single population for conservation purposes. Exchangeability of the populations, however, should not be used to promote homogenization of fish spawning in the different rivers. As some degree of genetic divergence was detected in this study, it is recommended that the spawning groups be treated as separate management units.

Applying molecular genetic tools to tiger conservation

The utility of molecular genetic approaches in conservation of endangered taxa is now commonly recognized. Over the past decade, conservation genetic analyses based on mitochondrial DNA sequencing and microsatellite genotyping have provided powerful tools to resolve taxonomy uncertainty of tiger subspecies, to define conservation units, to reconstruct phylogeography and demographic history, to examine the genetic ancestry of extinct subspecies, to assess population genetic status non-invasively, and to verify genetic background of captive tigers worldwide. The genetic status of tiger subspecies and populations and implications for developing strategies for the survival of this charismatic species both in situ and ex situ are discussed.

Genetic diversity of Pasteurella species isolated from European vespertilionid bats

Pasteurella are an important cause of fatal infections in free-ranging bats, but the genetic diversity of bat-derived strains is unclear. In the current study, 81 Pasteurella strains associated with pneumonia, severe organ necroses and systemic infection in free-ranging European vespertilionid bats were characterized by biochemical and molecular typing methods. Genetic relationships and subspecies status of Pasteurella multocida strains were determined by comparative 16S rDNA and rpoB gene sequence analysis. In addition, 30 representatives of the bat-derived P. multocida strains were selected based on phenotypic and genotypic tests to be compared by pulsed-field gel electrophoresis using SmaI. Most (85%) of the Pasteurella strains obtained from free-ranging bats in this study represented P. multocida ssp. septica. P. multocida ssp. multocida and Pasteurella species B were also identified in a small number of isolates. PFGE analysis correlated well with the sequencing results and revealed a high genetic diversity among bat-derived strains of P. multocida ssp. septica. Strains sharing identical or closely related SmaI fragment patterns were cultured from bats of different species, geographic origins, and years of isolation. The presence of numerous different P. multocida strains allows the assumption that Pasteurella infections in vespertilionid bats are not solely based on intra- but also on inter-species transmission. And indeed, our results present evidence of P. multocida infections in bats following cat predation.