Phylogeography Unplugged: Comparative Surveys in the Genomic Era

In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo-Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional ( unplugged ) approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches

Phylogeography Unplugged: Comparative Surveys in the Genomic Era

In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo- Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional (“unplugged”) approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches

Ciliopagurus vakovako Poupin 2001

Ciliopagurus vakovako Poupin, 2001 (Figs 1C; 3C; 4C; 6-9) Ciliopagurus vakovako Poupin, 2001: 292, figs 1a, 2a-d, 3b, 4 [type locality: Eiao I., Marquesas Is., French Polynesia]. Ciliopagurus krempfi – Forest 1995a: 59 (in part, only specimens from Marquesas) [not Ciliopagurus krempfi (Forest, 1952)]. Ciliopagurus strigatus – Forest 1995a: 50 (in part, only specimens from Marquesas) [not Ciliopagurus strigatus (Herbst, 1804)]. TYPE MATERIAL. — Marquesas Is., Eiao I., 1-2 m, 1 &male; holotype 4.3 mm (MNHN 5896), Nuku Hiva I., Anao bay. — Nuku Hiva I., 3 &male;&male;, 1 &female; paratypes (MNHN Pg 5897). — Ua Huka I., 2 &female;&female; paratypes (MNHN Pg 5898); 1 &female; paratype (leg to WAM); 2 &male;&male;, 2 &female;&female; paratypes, 1 paratype in shell (leg to ZRC). — Ua Pou I., 2 &male;&male; paratypes (MNHN Pg 5901). SHELLS. — Conidae: Conus tessulatus Born, 1778. Olividae: Oliva sp. MATERIAL EXAMINED. — French Polynesia. Marquesas Is, Eiao I., snorkelling 1-2 m, coll. J. Poupin, 7.IX.1997, 1 &male; 4.3 mm (holotype MNHN Pg 5896). — Nuku Hiva I., Anao bay, scuba diving at night, coll. P. Laboute, 21.IX.1997, 3 &male;&male; 3.4-6.2 mm, 1 &female; 2.8 mm (MNHN Pg 5897). — Nuku Hiva I., west side of Taiohae Bay, Marquesas Expedition, stn STA-NH-III, 1-3 m, 16.IX.1967, 1 &male; 5.3 mm, 1 &female; 5.5 mm (WAM C25048). — Tahuata I., FRV Marara, stn D47, 9°54.3’S, 139°06.5’W, dredge 48 m, 31.VIII.1990, 2 &female;&female; 1.4, 2.3 mm (MNHN Pg 5439). — Ua Huka I., Teuahia bay, MUSORSTOM 9, stn 25, 8°55.7’S, 139°36.7’W, dredge 6-15 m, coll. R. von Cosel, J. Tardy & J. Tröndlé, 16.IX-19.X.1997, 2 &female;&female; 1.6, 7.3 mm (MNHN Pg 5898, &female; 1.6 mm DNA H277- EF683563). — Hane bay, MUSORSTOM 9, stn 29, 8°55.7’S, 139°32.0’W, dredge 7-11 m, coll. von Cosel et al., 16.IX-19.X.1997, 1 &female; 3.7 mm (WAM leg. from MNHN collections). — Haavei bay, Tenoni point, “île aux Oiseaux” (Teuaua islet), MUSORSTOM 9, stn 34, c. 8°56.8’S, 139°35.7’W, dredge 10-15 m, coll. von Cosel et al., 16.IX-19.X.1997, 2 &male;&male; 1.2, 1.9 mm, 2 &female;&female; 2.3, 3.8 mm, 1 additional specimen in its shell (ZRC leg from MNHN collections). — Ua Pou I., MUSORSTOM 9, stn CP1264, 9°21.3’S, 140°07.7’W, 53-57 m, 3.IX.1997, 2 &male;&male; 3.2, 3.5 mm (MNHN Pg 5901, &male; 3.2 mm DNA H278- EF683564). DISTRIBUTION (Fig. 9). — French Polynesia, Marquesas Is. (Eiao I., Nuku Hiva I., Tahuata I., Ua Huka I., Ua Pou I.). Collected from the intertidal to 10-20 m, with a single record at 53- 57 m. DIAGNOSIS. — Ocular peduncles 0.60-0.77 times as long as shield (average 0.70). Distal segment of antennular peduncle 0.21-0.31 times as long as shield (average 0.27). Ocular acicles with 3-5 terminal spines, usually 4. Chelipeds equal; outer face of chelae with 3 complete transverse striae, 1 proximal striae interrupted near ventral margin of the palm and 2 short striae situated in ventral half between striae 1-2 and 2-3. These striae are smooth or with minute spinules. Chela 0.74-0.94 times as long as shield (average 0.84); ratio of height to length 0.60-0.98 (average 0.74); fingers 0.44-0.63 times as long as chela (average 0.54). Stridulating area with 4 distinct areas composed of parallel corneous crests; distal area the largest with 8-11 distally rounded or acute crests; 6th to 8th crest longest, about 0.50 times as long as stridulating area. Merus of cheliped without prominent tubercle on ventral surface. Dactyl of third ambulatory leg 0.90-1.16 times as long as propodus (average 1.07). Posterior lobes of telson subequal to moderately asymmetrical with 2-4 inconspicuous spines on terminal margins. COLORATION (Fig. 1C). — Antennular and antennal peduncles reddish-orange, flagella cream; ocular peduncles and ocular acicles reddish-orange, cornea black. Chelipeds (Fig. 3C) and ambulatory legs (Fig. 4C) with bright red rings alternating with narrower yellow rings. Chelipeds (Fig. 3) with red rings disposed on meri, carpi, and palms of chelae; fingers of chelae uniformly pale orange. Ambulatory legs (Fig. 4C) with red rings on meri, carpi and propodi; dactyls uniformly pale orange, terminal claws black. Shield cream with some light orange mottling on posterior half. Abdomen red, striped with undulating transverse, almost parallel yellow lines. REMARKS By its coloration Ciliopagurus vakovako cannot be confused with any species of the “ strigatus complex” (see Fig. 1). It bears some resemblance to C. tricolor, with similar pale orange colour on the fingers of chelae and dactyls of ambulatory legs, but the coloured rings disposed on the remaining parts of these appendages are uniformly red in C. vakovako instead of being bluish white and red in C. tricolor. Morphological characters used by Poupin (2001) to distinguish C. vakovako, C. strigatus and C. tricolor are not confirmed in this work by examination of more specimens of each species.The difference in the striation pattern of the outer face of chela between C. strigatus and C. vakovako (Poupin 2001: fig. 3) now clearly appears to be size related and is not confirmed for specimens of similar size (compare outer face of chelae in Figure 3A and 3C). Similarly, differences tentatively indicated by Poupin (2001) between C. vakovako and C. tricolor are not confirmed. In both species the posterior margins of both lobes of the telson can be unarmed or with few minutes spines (usually 1-4) and the proportion of the ocular peduncles are likewise in both species. In C. vakovako and C. tricolor, respectively, the mean length of ocular peduncle divided by shield length is 0.70 and 0.67 (see Table 1 and Fig. 8) and length of ocular peduncle divided by diameter of cornea is 4.60 and 4.97. The small differences between these means are not statistically significant (P<0.05). In conclusion, the possibility considered by Poupin (2001) that the minor morphological differences used to separate C. vakovako, C. tricolor, and C. strigatus are artifacts due to comparison of specimens of unequal size is confirmed in this study after examination of more specimens. Live coloration thus remains the only confident way to separate these species.Published as part of Poupin, Joseph & Malay, Maria Celia, 2009, Identification of a Ciliopagurus strigatus (Herbst, 1804) species-complex, with description of a new species from French Polynesia (Crustacea, Decapoda, Anomura, Diogenidae), pp. 209-232 in Zoosystema 31 (2) on pages 220-222, DOI: 10.5252/z2009n2a1, http://zenodo.org/record/539865

Identification of a Ciliopagurus strigatus (Herbst, 1804) species-complex, with description of a new species from French Polynesia (Crustacea, Decapoda, Anomura, Diogenidae)

Four hermit crabs of the genus Ciliopagurus are recognized as a complex of species named the “strigatus complex”. They are found in the low intertidal or shallow waters of the Indo-West Pacific. Ciliopagurus strigatus (Herbst, 1804) is characterized by striped legs and chelae with alternate yellow and red transverse colour bands. It is commonly found on reef habitats and is reported from the Red Sea to French Polynesia. Ciliopagurus tricolor Forest, 1995 is reported with certainty from East Africa to Réunion Island, C. vakovako Poupin, 2001 is endemic to the Marquesas Islands, and C. galzini n. sp. is described as a new species from specimens collected in the Tuamotus. Within the 17 extant species of the genius Ciliopagurus, these four species are distinct by the aspect of the ocular acicle with 3-5 terminal spines instead of usually 1 or 2 in the other species, a few morphometric characters, and by their vertical distribution, from intertidal to about 20 m, whereas all the other species are usually collected deeper. The species of the strigatus complex are morphologically very similar and can be separated with confidence only by their coloration. All of them have similar colour patterns of transverse bands on the cheliped and walking legs, but each species can be easily recognized by the distinct colour and/or disposition of these bands. The appraisal of these colour differences as valuable specific indicators is confirmed by phylogenetic analysis of mitochondrial and nuclear DNA sequences

Peripatric speciation drives diversification and distributional pattern of reef hermit crabs (Decapoda: Diogenidae: Calcinus)

The diversity on coral reefs has long captivated observers. We examine the mechanisms of speciation, role of ecology in speciation, and patterns of species distribution in a typical reef‐associated clade—the diverse and colorful Calcinus hermit crabs—to address the origin of tropical marine diversity. We sequenced COI, 16S, and H3 gene regions for ∼90% of 56 putative species, including nine undescribed, “cryptic” taxa, and mapped their distributions. Speciation in Calcinus is largely peripatric at remote locations. Allopatric species pairs are younger than sympatric ones, and molecular clock analyses suggest that \u3e2 million years are needed for secondary sympatry. Substantial niche conservatism is evident within clades, as well as a few major ecological shifts between sister species. Color patterns follow species boundaries and evolve rapidly, suggesting a role in species recognition. Most species prefer and several are restricted to oceanic areas, suggesting great dispersal abilities and giving rise to an ocean-centric diversity pattern. Calcinus diversity patterns are atypical in that the diversity peaks in the west-central oceanic Pacific rather than in the Indo-Malayan diversity center. Calcinus speciation patterns do not match well-worn models put forth to explain the origin of Indo-West Pacific diversity, but underscore the complexity of marine diversification

Reconnaissance d’espèces jumelles proches de &lt;i&gt;Ciliopagurus strigatus&lt;/i&gt; (Herbst, 1804), avec la description d’une nouvelle espèce de Polynésie française (Crustacea, Decapoda, Anomura, Diogenidae)

Quatre Bernard-l’ermite du genre Ciliopagurus sont identifiés comme appartenant à un complexe d’espèces nommé « complexe strigatus ». Ils sont récoltés dans le bas de la zone intertidale et par petits fonds dans tout l’Indo-ouest Pacifique. Ciliopagurus strigatus (Herbst, 1804) est caractérisé par des rayures sur les pinces et les pattes ambulatoires. Il est commun des récifs, depuis la mer Rouge jusqu’à la Polynésie française. Ciliopagurus tricolor Forest, 1995 est connu avec certitude de l’Afrique orientale à l’île de la Réunion, C. vakovako Poupin, 2001 est endémique des îles Marquises, et C. galzini n. sp. est décrit comme une nouvelle espèce à partir de spécimens récoltés dans les Tuamotu. Parmi les 17 espèces actuelles du genre Ciliopagurus, ces quatre espèces sont distinctes par : l’écaille oculaire terminée par 3-5 épines, au lieu de 1 ou 2 épines pour toutes les autres espèces, quelques caractères biométriques, et leur distribution verticale, depuis le milieu intertidal jusqu’à environ 20 m, alors que toutes les autres espèces sont généralement récoltées plus profond. Elles sont morphologiquement très proches et ne peuvent être reconnues facilement que par leur coloration. Toutes ont des bandes colorées transverses sur les pinces et les pattes ambulatoires mais chaque espèce présente des couleurs distinctes ou une disposition particulière des bandes. L’utilisation de ces différences de coloration comme caractère spécifique valable est confirmée par des analyses phylogénétiques de l’ADN mitochondrial et nucléaire.Four hermit crabs of the genus Ciliopagurus are recognized as a complex of species named the “strigatus complex”. They are found in the low intertidal or shallow waters of the Indo-West Pacific. Ciliopagurus strigatus (Herbst, 1804) is characterized by striped legs and chelae with alternate yellow and red transverse colour bands. It is commonly found on reef habitats and is reported from the Red Sea to French Polynesia. Ciliopagurus tricolor Forest, 1995 is reported with certainty from East Africa to Réunion Island, C. vakovako Poupin, 2001 is endemic to the Marquesas Islands, and C. galzini n. sp. is described as a new species from specimens collected in the Tuamotus. Within the 17 extant species of the genus Ciliopagurus, these four species are distinct by the aspect of the ocular acicle with 3-5 terminal spines instead of usually 1 or 2 in the other species, a few morphometric characters, and by their vertical distribution, from intertidal to about 20 m, whereas all the other species are usually collected deeper. The species of the “strigatus complex” are morphologically very similar and can be separated with confidence only by their coloration. All of them have similar colour patterns of transverse bands on the chelipeds and walking legs, but each species can be easily recognized by the distinct colour and/or disposition of these bands. The appraisal of these colour differences as valuable specific indicators is confirmed by phylogenetic analysis of mitochondrial and nuclear DNA sequences.</p

Peripatric speciation drives diversification and distributional pattern of reef Hermit Crabs (Decapoda: Diogenidae: Calcinus)

The diversity on coral reefs has long captivated observers. We examine the mechanisms of speciation, role of ecology in speciation, and patterns of species distribution in a typical reef-associated clade-the diverse and colorful Calcinus hermit crabs-to address the origin of tropical marine diversity. We sequenced COI, 16S, and H3 gene regions for similar to 90% of 56 putative species, including nine undescribed, "cryptic" taxa, and mapped their distributions. Speciation in Calcinus is largely peripatric at remote locations. Allopatric species pairs are younger than sympatric ones, and molecular clock analyses suggest that > 2 million years are needed for secondary sympatry. Substantial niche conservatism is evident within clades, as well as a few major ecological shifts between sister species. Color patterns follow species boundaries and evolve rapidly, suggesting a role in species recognition. Most species prefer and several are restricted to oceanic areas, suggesting great dispersal abilities and giving rise to an ocean-centric diversity pattern. Calcinus diversity patterns are atypical in that the diversity peaks in the west-central oceanic Pacific rather than in the Indo-Malayan "diversity center." Calcinus speciation patterns do not match well-worn models put forth to explain the origin of Indo-West Pacific diversity, but underscore the complexity of marine diversification

New distribution record of Habenaria gibsonii var. foetida Blatt. & McCann (Orchidaceae, Orchidoideae) from Panay Island, Philippines, with notes on allied taxa, ecology, and conservation

We report the occurrence of Habenaria gibsonii var. foetida Blatt. & McCann on Panay Island in the Philippines. Our new records represent the easternmost distribution of this species, and also the first in the Malesian region. We present a full description, photographs, updated distribution map, and notes on allied taxa, ecology, and conservation status of this taxon. Our report highlights the importance of Panay Island in floristic studies of the Philippines

FIGURE 3. Pseudopaguristes flavioculus n in A new species of the diogenid hermit crab genus Pseudopaguristes McLaughlin 2002 from the Northern Mariana Islands, Micronesia

FIGURE 3. Pseudopaguristes flavioculus n. sp., holotype, male (sl 2.7 mm), SIO-BIC C14508. A, right chela, dorsal view; B, carpus of right cheliped, dorsal view; C, left chela, dorsal view; D, carpus of left cheliped, dorsal view; E, dactylus of right pereopod 2, mesial view; F, dactylus of left pereopod 3, mesial view; G, dactylus to carpus of left pereopod 4, lateral view; H, dactylus of left pereopod 4 (setae omitted); I, merus and ischium of left pereopod 4, mesial view (setae omitted); J, close up of one of setae on ventrodistal angle of pereopod 4 carpus; K, left pleopod 1, ventral view; L, left pleopod 2, ventral view; M, distal article of left pleopod 2, mesial view; N, same, dorsal view.Published as part of &lt;i&gt;Komai, Tomoyuki, Miller, Allison K. &amp; Malay, Maria Celia D., 2022, A new species of the diogenid hermit crab genus Pseudopaguristes McLaughlin 2002 from the Northern Mariana Islands, Micronesia, pp. 570-582 in Zootaxa 5175 (5)&lt;/i&gt; on page 576, DOI: 10.11646/zootaxa.5175.5.6, &lt;a href="http://zenodo.org/record/7009572"&gt;http://zenodo.org/record/7009572&lt;/a&gt

Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia

Komai, Tomoyuki, Miller, Allison K., Malay, Maria Celia D. (2022): Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia. Zootaxa 5099 (5): 563-585, DOI: 10.11646/zootaxa.5099.5.