Morphological study of goby (gobiidae) from Lombok Island – Indonesia

MORPHOLOGICAL STUDY OF GOBY (GOBIIDAE) FROM
LOMBOK ISLAND – INDONESIA

YULIADI ZAMRONI

POST GARDUATE SCHOOL
BOGOR AGRICULTURAL UNIVERSITY
BOGOR
2011

i

STATEMENT OF THESIS
AND INFORMATION SOURCE
Hereby I express that the thesis entitled: Morphological study of goby
(Gobiidae) from Lombok Island – Indonesia is the original result of my research
and has never been published. All data and information I provided in the thesis are
based on evidence and available references.

Bogor, March 2011

Yuliadi Zamroni
NRP G352080011

ii

ABSTRAK
YULIADI ZAMRONI. Studi Morfologi Ikan Gobi (Gobiidae) dari Pulau
Lombok - Indonesia. Dibimbing oleh BAMBANG SURYOBROTO dan
MOHAMMAD MUKHLIS KAMAL.
Studi morfologi ikan gobi telah dilakukan berdasarkan 22 karakter
morfometrik dan 8 karakter meristik. Ikan gobi dikoleksi dari enam lokasi di
Pulau Lombok, tiga lokasi di sungai (Jangkuk, Sidutan, dan Belimbing) dan tiga
lokasi di hutan mangrove (Selindungan, Teluk Sepi, dan Labuan Treng). Sampel
dikoleksi dengan menggunakan electro-fishing (12 V, 10 A) untuk ikan gobi
diperairan sungai dan campuran minyak cengkeh dan alkohol 50% (1 : 3 bagian)
sebagai anastesi untuk ikan gobi diperairan mangrove. Dari hasil identifikasi,
didapatkan 21 spesies ikan gobi. Analisis pengelompokan menunjukkan ikan gobi
dapat dikelompokkan menjadi 7 kelompok yang merujuk pada level genus, antara
lain Acentrogobius (kelompok 1), Amoya (kelompok 2), Periophthalmus
(kelompok 3), Stiphodon (kelompok 4), Sicyopterus (kelompok 5),

Boleophthalmus (kelompok 6), dan Oxyurichthys (kelompok 7). Dari 22 karakter
morfometrik dan 8 karakter meristik, didapatkan 6 karakter morfometrik (panjang
moncong sampai sirip ventral, panjang batang ekor, panjang dasar dari sirip dorsal
ke-2, panjang dasar dari sirip anal, panjang sirip ventral, dan panjang postorbital)
dan 2 karakter meristik (jumlah sisik lateral dan jumlah sisik predorsal)
memberikan variasi yang tinggi pada data sehingga karakter ini sangat baik
digunakan sebagai karakter taksonomi untuk mengelompokkan ikan gobi.
Kata kunci : Ikan gobi, pengelompokan, morfologi, pulau Lombok

iii

SUMMARY
YULIADI ZAMRONI. Morphological study of goby (Gobiidae) from Lombok
Island – Indonesia. Supervised by BAMBANG SURYOBROTO, MOHAMMAD
MUKHLIS KAMAL.
Gobies (family Gobiidae) are bottom-dwelling fishes with flattened head,
rounded snout, and bulbous cheeks that having a characteristic of two soft-spined
dorsal fins and united ventral fins (disc-like) adapted to bottom-living life style.
These modified fins are sucker device which enable the fish to grasp on surfaces
and prevent from drifting in fast water current. Gobies are one of fish group who

dominate ocean islands because of amphidromous larvae stage, euryhalinity, small
size, an excellent climbing ability, a wide range of trophic level, frequent lack of
gas bladder, and an associated bottom-living life style.
Taxonomically, Gobiidae is one of the most poorly known family and
consists of numerous undescribed species. There are many unanswered question
about them, such as how many species there are and their phenetic relationship.
Morphological study can be used to clustering and understanding relationship of
taxa. Variation in morphological data can be used to characterize the distance
between them. The distance makes each taxon uniquely diagnosable
Lombok is an ocean island and present study analyze samples of gobies that
were collected from six locations in Lombok. They were three locations at rivers
(Jangkuk, Sidutan and Belimbing) and three locations at mangrove forests
(Selindungan, Sepi Bay, and Labuan Treng). Electric fishing gear (12 V, 10 A)
was employed for about one hour per location in rivers, whereas in mangrove
forest sampling was carried out using anaesthetic during low tide in pools and
creeks. A mixture of one part clove oil and three parts of 50% alcohol was used as
anaesthetic agent.
Morphometric and meristic data have been analyzed using R software
version 2.12.1. The morphometric measurements were standardized on Standard
Length (SL) to remove size effect. These morphological data were analyzed using

Principal Components Analysis (PCA) to remove the correlation between
variables.
Clustering of gobies was performed using K-means method to select a
prespecified number of cluster centers to minimize the within-class sum of
squares from those centers. This analysis was followed with elbow criterion
method to estimate the best number of clusters. The criterion used the ratio of
within-group to the total variances. The best number of clusters could be
estimated when adding a group did not improve the explained variance, and the
closeness between clusters were estimated using Minimum Spanning Tree (MST).
Based on morphological identification result, 214 specimens of gobies from
Lombok could be distinguished into 21 species in 10 genera and 4 subfamilies. In
this study, 12 species were included in analysis and 9 species were excluded
because consisting of only few samples. However, after clustering 12 species, 9
species which were excluded in analysis were plotted in principal component
space to find their relation with other clusters.
Cluster analysis result showed clustering of gobies into seven clusters
(reffered to genera level). They were Acentrogobius (1st cluster), Amoya (2nd

iv

cluster), Periophthalmus (3rd cluster), Stiphodon (4th cluster), Sicyopterus (5th
cluster), Boleophthalmus (6th cluster), and Oxyurichthys (7th cluster). These
specimens had six morphometric characters (snout to ventral fins length, caudal
peduncle length, 2nd dorsal fin base length, anal fin base length, ventral fin length,
and postorbital length) and two meristic characters (lateral scale rows and
predorsal scale rows) gave higher variation and good as taxonomic characters to
separate the taxa.

Key words : Gobies, Lombok, Morphology, Clustering

v

Copyright©2011 by Bogor Agricultural University
Copyright are protected by law,
1.
It is prohibited to cite all or part of this thesis/ dissertation without referring
to and mentioning the source.
a. Citation only permitted for sake of education, research, scientific
problem.
b. Citation doesn’t inflict the name and honor of Bogor Agricultural

University.
2.
It is prohibited to republish and reproduce all or part of this thesis/
dissertation without the written permission from Bogor Agricultural
University.

vi

MORPHOLOGICAL STUDY OF GOBY (GOBIIDAE) FROM
LOMBOK ISLAND – INDONESIA

YULIADI ZAMRONI

Thesis
As partial fulfillment of the requirements for Master Degree in Animal
Biosciences

POST GARDUATE SCHOOL
BOGOR AGRICULTURAL UNIVERSITY
BOGOR

2011

vii

Extra-committee examiner : Dr. Ir Achmad Farajallah, M.Si

viii

Title

: Morphological Study of Goby (Gobiidae) from Lombok
Island- Indonesia

Name

: Yuliadi Zamroni

Registration number : G352080011

Certified by:

Advisory committee

Dr. Bambang Suryobroto
Chairman

Dr. Ir. Mohammad Mukhlis Kamal, M.Sc
Member

Acknowledged by

Coordinator
Major of Animal Biosciences

Dean of Postgraduate School

Dr. Bambang Suryobroto

Dr. Ir. Dahrul Syah, M.Sc.Agr

Date of Examination: March, 24th 2011

Date of Graduation:

ix

O man! What has deluded you in respect of your Noble Lord?
He Who created you and formed you and proportioned you and assembled you
in whatever way He willed.
(Al-Qur’an, Surat al-Infitar: 6-8)

THIS THESIS IS DEDICATED TO
INDONESIAN MARINE TAXONOMY SOCIETY (IMTS)

x

FOREWORD

On the blessing of God I am able to finish my thesis. This paper is made to
fulfill the requirement for master degree at Bogor Agricultural University. The

title of my paper is “Morphological Study of Goby (Gobiidae) from Lombok
Island- Indonesia”.
I would like to thank my advisor committee Dr. Bambang Suryobroto and
Dr. Mohammad Mukhlis Kamal. I am indebted to Dikti Depdiknas for the
Postgraduate Scholarship (BPPS); Indonesian Institute of Science and
Conservation International Indonesia for the sponsored my training in Indonesian
Marine Taxonomy; and Raffles Museum for allowing me to study of gobies.
Special thank to Dr. Zeehan Jaafar (Nasional University of Singapore,
Singapore) and Dr. Helen Larson (Museum and Art Gallery of The Northern
Territory, Australia) for introduce to me how to identified of gobies, collecting
methods, and all of gobies information. I express my gratitude to Novita Tri
Artiningrum (my wife), Annisa Hishnul Izza (my daughter), Andy Darmawan (my
friend), and Mrs Tini and Ani (laboratory assistant) for their support.
May this paper is usefull for all who study on gobies taxonomy.

Bogor, March 2011

Yuliadi Zamroni

xi

CURRICULUM VITAE
The author was born in Mataram on July 10th, 1981 as the seventh son of
Masyhur Hamnur (†) and Saidah. The author got married with Novita Tri
Artiningrum and have one daughter (Annisa Hishnul Izza).
Under graduate course was carried out in 1999 until 2003 at Biology
Faculty in Jenderal Soedirman University, Purwokerto. Since 2005, the author has
been working as a lecturer in Biology Study Program, Faculty of Mathematics and
Natural Science, Mataram University, in Mataram. In 2008, the author continued
study at the School of Postgraduate, Bogor Agricultural University that sponsored
by the Dikti Depdiknas postgraduate scholarship (BPPS).

xii

CONTENTS

Page
LIST OF TABLE .............................................................................................. xiii
LIST OF FIGURE ............................................................................................ xiv
LIST OF APPENDIX....................................................................................... xvii
INTRODUCTION ............................................................................................... 1
LITERATURE STUDY
Taxonomic Remarks of Gobies ........................................................................ 3
Lombok Gobies ............................................................................................... 3
Morphological Analysis ................................................................................... 4
MATERIALS AND METHODS
Study Site ........................................................................................................ 5
Sample Collection ............................................................................................ 5
Gobies Identification ........................................................................................ 6
Morphometric data ........................................................................................... 7
Meristic data .................................................................................................... 9
Data Analysis ................................................................................................. 10
CLUSTER ANALYSIS
Clustering of Gobies Based on Morphometric Characters............................... 11
Clustering of Gobies Based on Meristic Characters ........................................ 14
IDENTIFICATION ............................................................................................ 17
DISCUSSION.................................................................................................... 42
CONCLUSION ................................................................................................. 45
LITERATURES CITED..................................................................................... 46
APPENDIX ....................................................................................................... 50

xiii

LIST OF TABLES
Page
1 Twenty one species in this study....................................................................... 7
2 List of morphometric characters of gobies used in this study ............................ 8
3 List of meristic characters of gobies used in this study ................................... 10
4 Percentage of variance explainable with adding number of clusters ................ 11
5 Eigen value, proportion of variance, and cumulative of variance. ................... 13
6 Eigen vector of each character on first two PCs. ............................................. 14
7 Percentage of variance explainable with adding number of clusters. ............... 14
8 Eigen value, proportion of variance, and cumulative of variance. ................... 16
9 Eigen vector of each character on PC1 and PC2. ............................................ 16

xiv

LIST OF FIGURES
Page
1 Map of sampling areas: (A) Jangkuk river, (B) Sidutan river, (C) Belimbing
river, (D) Labuan Treng mangrove forest, (E) Selindungan mangrove forest,
and (F) Sepi Bay mangrove forest. ................................................................ 6
2 Morphometric characters of gobies. ................................................................. 7
3 Meristic characters (A) scale counts: LSR (red), TSR (yellow) and PSR (blue).
(B) Fin-ray count........................................................................................... 9
4 Plotting of all speciments in two first PC indicate centroid of clusters and their
minimum spanning tree ............................................................................... 12
5 Plotting of all speciments in two first PC indicate centroid of clusters and their
minimum spanning tree ............................................................................... 15
6 Ventral view of pelvic fins (a) Without frenum; (b) Frenum without fleshy lobes;
(c) Frenum with fleshy lobes ....................................................................... 17
7 (a) Ventral fins with frenum and fleshy lobes; (b) eyes lateral and without eyelid
................................................................................................................... 18
8 Head pores type (a) A pair and (b) A single of anterior interorbital pore(s)..... 18
9 Dermal crest on top of head. ........................................................................... 19
10 Tongue distinctly bilobed. ............................................................................ 19
11 Acentrogobius audax, 43.33 mm in SL, Selindungan, Sekotong distric-western
Lombok. ..................................................................................................... 20
12 Acentrogobius janthinopterus, 49.87 mm in SL, Sepi Bay, Sekotong districwestern Lombok. ........................................................................................ 20
13 Acentrogobius viridipunctatus, 66.14 mm in SL, Selindungan, Sekotong
distric-western Lombok............................................................................... 21
14 Amoya gracilis, 42.35 mm in SL, Labuan Treng, Labuan distric-western
Lombok. ..................................................................................................... 22
15 Amoya moloana, 44.83 mm in SL, Selindungan, Sekotong distric-western
Lombok. ..................................................................................................... 23
16 Amoya raveni, 45.08 mm in SL, Labuan Treng, Labuan distric-western
Lombok. ..................................................................................................... 23

xv

17 Cristatogobius rubripectoralis, 49.80 mm in SL, Selindungan, Sekotong
distric- western Lombok.............................................................................. 24
18 Glossogobius celebius, 47.00 mm in SL, Sidutan River, Kayangan districnorthern Lombok. ....................................................................................... 25
19 Dorsal view of head ..................................................................................... 26
20 Oxyurichthys tentacularis, 66.96 mm in SL, Labuan Treng, Labuan districwestern Lombok. ........................................................................................ 27
21 Oxyurichthys ophthalmonema, 41.51 mm in SL, Selindungan, Sekotong
distric-western Lombok............................................................................... 28
22 Pseudogobius javanicus, 27.75 mm in SL, Selindungan, Sekotong districwestern Lombok. ........................................................................................ 29
23 Ventral view of head showing (a) black branchiostegal membranes and (b)
pale brachiostegal membrans....................................................................... 30
24 Boleophthalmus boddarti, 89.94 mm in SL, Labuan Treng, Labuan districtwestern Lombok. (A) Male 1st dorsal fin, (B) Female 1 st dorsal fin, and (C)
Ventral fins with frenum. ............................................................................. 31
25 Periophthalmus argentilineatus, 37.85 mm in SL, Sepi Bay, Sekotong districwestern Lombok. (A) First and second dorsal fins and (B) Ventral fin without
frenum. ....................................................................................................... 32
26 Periophthalmus gracilis, 33.45 mm in SL, Sepi Bay, Sekotong distric-western
Lombok. (A) First and second dorsal fins and (B) Ventral fin without frenum.
................................................................................................................... 33
27 Periophthalmus malaccensis, 69.28 mm in SL, Sepi Bay, Sekotong districwestern Lombok. (A) First and second dorsal fin, (B) Ventral view of head
showing pale branchiostegal membranes and ventral fin with frenum. ......... 34
28 Periophthalmus minutus, 41.55 mm in SL, Sepi Bay, Sekotong. (A) First and
second dorsal fin, (B) Ventral fin without frenum. ....................................... 35
29 Periophthalmus novemradiatus, 88.46 mm in SL, Sepi Bay, Sekotong districwestern Lombok. (A) First and second dorsal fins, first sipine at D1 elongate,
(B) Ventral view of head showing black branchiostegal membranes and
ventral fins with frenum. ............................................................................. 36
30 Pelvic disc (a) not adherent to belly in Stiphodon and (b) adheren in
Sicyopterus. ................................................................................................ 37
31 Upper lip view (a) with cleft and (b) with papillose ...................................... 38

xvi

32 (A) Sicyopterus cyanocephalus, 65.33 mm in SL, Belimbing River, eastern
Lombok, (B) Ventral view of head showing clefts in upper lip and frenum at
ventral fins with fleshy lobes. ...................................................................... 38
33 (A) Sicyopterus hageni, 51.35 mm in SL, Sidutan River, northern Lombok,
(B) Ventral view of head showing clefts in upper lip and frenum at ventral
fins with fleshy lobes. ................................................................................. 39
34 (A) Sicyopterus microcephalus, 45.72 mm in SL, Jangkuk River, Mataram,
(B) Ventral view of head showing clefts in upper lip and frenum at ventral
fins with fleshy lobes. ................................................................................. 40
35 Stiphodon elegans (female), 26.75 mm in SL, Jangkuk River, Mataram. ...... 40

xvii

LIST OF APPENDIXES
Page
1 Clustering of gobies based on morphomrtric data. ......................................... 51
2 Clustering of gobies based on meristic data. .................................................. 53
3 Morphometric and Meristic Data of Acentrogobius audax (n=5). .................. 55
4 Morphometric and Meristic Data of Acentrogobius janthinopterus (n=20). ... 56
5 Morphometric and Meristic Data of Acentrogobius viridipunctatus (n=21). ... 57
6 Morphometric and Meristic Data of Amoya gracilis (n=13). .......................... 58
7 Morphometric and Meristic Data of Amoya moloana (n=11). ........................ 59
8 Morphometric and Meristic Data of Amoya raveni (n=12). ............................ 60
9 Morphometric and Meristic Data of Cristatogobius rubripectoralis (n=2). .... 61
10 Morphometric and Meristic Data of Glossogobius celebius (n=1). ................. 62
11 Morphometric and Meristic Data of Oxyurichthys tentacularis (n=14). ......... 63
12 Morphometric and Meristic Data of Oxyurichthys ophthalmonema (n=3). ..... 64
13 Morphometric and Meristic Data of Pseudogobius javanicus (n=6). .............. 65
14 Morphometric and Meristic Data of Boleophthalmus boddarti (n=12). .......... 66
15 Morphometric and Meristic Data of Periophthalmus argentilineatus (n=14).. 67
16 Morphometric and Meristic Data of Periophthalmus gracilis (n=5). .............. 68
17 Morphometric and Meristic Data of Periophthalmus malaccensis (n=1). ....... 69
18 Morphometric and Meristic Data of Periophthalmus minutus (n=3). ............. 70
19 Morphometric and Meristic Data of Periophthalmus novemradiatus (n=6). ... 71
20 Morphometric and Meristic Data of Sicyopterus cyanocephalus (n=12). ....... 72
21 Morphometric and Meristic Data of Sicyopterus hageni (n=12). .................... 73
22 Morphometric and Meristic Data of Sicyopterus microcephalus (n=25). ........ 74
23 Morphometric and Meristic Data of Stiphodon elegans (n=16). ..................... 75

INTRODUCTION
Gobies (family Gobiidae) are bottom-dwelling fishes with flattened head,
rounded snout, and bulbous cheeks that having a characteristic of two soft-spined
dorsal fins and united ventral fins (disc-like) adapted to bottom-living life style.
These modified fins are sucker device which enable the fish to grasp on surfaces
and prevent from drifting in fast water current (Koumans 1931; Larson & Lim
2005). They have a wide spectrum habitats covering the sea-floor at a depth of
over 300m below surface to mountain streems. Adaptations to these habitats lead
to various morphological specializations. Gobies lives on rock bottoms have short
round ventral fins sucker, whereas gobies lives on sandy and unstable bottoms
have large ventral fins sucker (Akihito et al. 2000).
Gobies dominate ocean islands. This condition was inferred from
amphidromous larvae stage, euryhalinity, small size, an excellent climbing ability,
a wide range of trophic level, frequent lack of gas bladder, and an associated
bottom-living life style (Ryan 1991).
Gobies comprise of approximately 2000 species in over 200 genera (Nelson
2006). Larson et al. (2008) reported 134 species of gobies found in Singapore;
Kottelat & Whitten (1993) found 18 species of freshwater gobies from Sumatera,
17 species from Borneo (5 species were endemic), 19 species from Java (2 species
were endemic) and 22 species from Celebes (9 species were endemic); Haryono &
Tjakrawidjaja (2004) found 12 species of freshwater gobies in Northern Celebes.
New Guinea was reported to have 300 species of gobies, 50 species of them were
found in freshwater (Allen 1991), and 11 species of freshwater gobies were found
in Timika region (Allen et al. 2000).
Lombok is one of oceanic islands in Lesser Sunda archipelago, located in
the southern Wallacea. Geologically, it was formed from under sea mountain
(Monk et al. 2000) and never be a part of mainland in Sundaland or Sahulland
(Cracraft 1988), so all fauna (including freshwater fishes) living in Lombok were
migrated through the sea.
The

morphological

adaptations

give

variation

in

morphological

measurements (quantitative) and meristic (qualitative) data which can be used to

2

characterize the phenetic distance between them. The distance may makes each
taxon uniquely identifiable. The focus of this research is observing and analysing
variations on morphological data in Lombok gobies.
The samples were collected from six locations in Lombok. They were three
locations at rivers (Jangkuk, Sidutan and Belimbing) and three locations at mangrove
forests (Selindungan, Sepi Bay, and Labuan Treng). Electric fishing gear (12 V, 10

A) was employed for about one hour per location in rivers, whereas in mangrove
forest sampling was carried out using anaesthetic agent during low tide in pools
and creeks. A mixture of one part clove oil and three parts of 50% alcohol was
used as anaesthetic.
These specimens could be classified based on morphometric variations into
seven clusters. They were Acentrogobius (1st cluster), Amoya (2nd cluster),
Periophthalmus argentilineatus (3rd cluster), Stiphodon elegans (4th cluster),
Sicyopterus (5th cluster), Boleophthalmus boddarti (6th cluster), and Oxyurichthys
tentacularis (7th cluster). These specimens had six morphometric characters (snout
to ventral fins length, caudal peduncle length, 2nd dorsal fin base length, anal fin
base length, ventral fin length, and postorbital length) and two meristic characters
(lateral scale rows and predorsal scale rows) gave higher variation and good as
taxonomic characters to separate the taxa.

LITERATURE REVIEW
Taxonomic Remarks of Gobies
Taxonomy of Gobiidae are highly complex and volatile. Gobies were
identified by Linnaeus (1759) based on “Caput poris 2 inter oculos approximatos
: altero anteriore, membr. branch. radiis IV, pinnae ventrales unitae in ovatam 12radiatam.”. He grouped these fishes into division III Pisces Thoracici under genus
Gobius. Seven species were included into this genus, they were G. anguillaris, G.
aphya, G. eleotris, G. jozo, G. niger, G. paganellus, and G. pectinirostris. The
earliest classification system of gobies interrelationship was proposed by Günther
(1861). He identified four groups of gobies, they were Amblyopina, Callionymina,
Gobiinae, and Trypauchenina
Regan (1911) identified these fishes based on osteology. This system
divided gobies into three families: Eleotridae, Gobiidae, and Psammichthyidae.
The Gobiidae were divided into two subfamilies, Gobiinae and Periophthalminae.
Major revision on family Gobiidae was carried out by Koumans (1931) who
analyzed the family by the presence of united ventral fins. He divided the extant
species

into

six

subfamilies:

Apocrypteinae,

Gobiinae,

Gobiodontinae,

Periophthalminae, Sicydiaphiinae, and Tridentigerinae. Partial taxonomy revision of
these fishes were studied by Murdy (1989) for Oxudercinae; Pezold (1993) for
Gobiinae; Parenti & Maciolek (1993) and Keith et al (2010) for Sicydiinae.
In the latest holistic study of these families, Larson & Murdy (2001) identified
approximately 500 species of 100 genera in the Western Central Pacific. They
identivied five subfamilies: Amblyopinae, Gobiinae, Gobionellinae, Oxudercinae, and
Sicydiinae.

Lombok Gobies
Lombok is the second highest island in Western Lasser Sunda after the
neighboring Sumbawa Island. For the most part, the western part of Lombok is
mountainous and hilly with lowland and plateau. Lombok is bordered by Java Sea on
north, Indian Ocean on south, Lombok Strait on west and Alas Strait on east
(Bakosurtanal 2004).

4

Geologically, Lombok is one of oceanic islands in the Wallacea region
which was formed from undersea mountains located in the middle of Indonesia,
between Sundaland and Sahulland (Monk et al. 2000). Based on geological time,
the islands in Wallace region (include Lombok island) are classified as very young
islands (15-1 mya) and never be a part of mainland in Sundaland or Sahulland.
The flora and fauna between the continent of Asia and Australia have never been
linked (Cracraft 1988). At least faunas living in Wallacea region (include Lombok
Island) migrated through the sea.
The distribution of fishes (especially of freshwater fishes)

in oceanic

islands are strongly correlated with the islands geology (Allen 1991). All fishes
inhabit these islands must migrated from the main islands through the sea. So, all
fishes living in this area have a diadromy lifestyle. Diadromy is migrated of fishes
between the sea and freshwater (McDowall 2007). Gobiidae is one of fish family
which diadromy lifestyle. Some gobies were reported found at Lesser Sundas by
Monk et al. (2000). The authours recorded several genera that founded in Lesser
Sundas, i.e. Acentrogobius, Awaous, Bathygobius, Glossogobius, Hemigobius,
Oxyurichthys, Pseudogobius, Sicyopterus, Stenogobius, and Stiphodon, but there
is no specific data which explain that gobies in this location.
Morphological Analysis
Gobies have many variations in size and shape. These variations can be
used as data to study of morphology between individuals, populations, species,
and higher taxa. Morphological data can be divided into morphometric and
meristic. Morphometric is continuous data from measured structure whereas
meristic is discrete data from countable structure (Helfman et al 2002).
Both morphometric and meristic data can be clustered by many methods,
one of them is K-means. K-means is method of cluster analysis which aims to
devide n observations into k clusters, so that the data have similar character within
cluster and different from the other clusters (Agusta 2007). K-means method is
better than other methods to analyze large and continuous data type. This method
clusters many objects and their outliers quickly (Claude 2008).

MATERIALS AND METHODS
Study Site
This study was conducted during January-October 2010. Fish samples were
collected from rivers and mangrove forests ecosystem in Lombok Island. In
rivers, samples were collected from three locations. They were Jangkuk river in
Mataram City, Sidutan river in northern Lombok, and Belimbing river in eastern
Lombok. Sampling location in mangrove forests were Sepi Bay and Selindungan
Village in Sekotong district, and Labuan Treng in Labuan district. Both Sekotong
and Labuan are located in the western Lombok (Figure 1). Gobies identification
and data analysis were conducted at Laboratory of Elementary Biology on
Mathematics and Natural Science Faculty in Mataram University and
Biosystematic

and

Animal

Ecology

Laboratory,

Biology

Department,

Mathematics and Natural Science Faculty of Bogor Agricultural University.

Sample Collection
Sampling was carry out in the morning and afternoon at river and mangrove
forest. Electric fishing gear (12 V, 10 A) was employed for about one hour per
location in rivers, whereas in mangrove forest sampling was carried out using
anaesthetic agent during low tide in pools and creeks. A mixture of one part clove
oil and three parts of 50% alcohol was used as anaesthetic. The gobies were
subsequently caught using a hand net (Wen et al. 2005; Imanpoor et al. 2010;
Robertson & Smith-Vaniz 2010). Gobies were fixed by formalin 4% and
preserved in alcohol 70% (Kottelat & Whitten 1993; Alonso 2001; Rachmatika et
al. 2004a; Rachmatika et al. 2004b; Haryono 2007). These gobies were deposited
at laboratory of Elementary Biology in Mataram University for identification.

6

Figure 1

Map of sampling areas: (A) Jangkuk river, (B) Sidutan river, (C)
Belimbing river, (D) Labuan Treng mangrove forest, (E) Selindungan
mangrove forest, and (F) Sepi Bay mangrove forest.

Gobies Identification
Identification to genera based on Larson & Murdy (2001). Identification to
species based on Koumans (1953), Whitley (1953), Akihito & Meguro (1975),
Akihito & Meguro (1976), Sakai & Nakamura (1979), Murdy (1989), Kottelat &
Whitten (1993), Allen (1991), Allen et al. (2000), Akihito & Meguro (2000),
Akihito et al. (2003), Haryono & Tjakrawidjaja (2004), Larson & Takita (2004),
Larson & Lim (2005), and Jaafar & Larson (2008). Based on morphological
identification result, 214 specimens of gobies from Lombok could be
distinguished into 21 species in 10 genera and 4 subfamilies. In this study, 12
species (B, C, D, E, F, G, K, L, R, S, T, and U) were included in analysis and 9
species (A, H, I, J, M, N, O, P, and Q) were excluded because consisting of only
few samples (Table 1). However, after clustering 12 species, 9 species which were

7

excluded in analysis were plotted in principal component space to find their
relation with other clusters.

Table 1 Twenty one species in this study
Code

Amount of
specimens

Species

Code

Amount of
specimens

Species

A
B
C
D
E
F
G
H
I
J
K

5
20
21
13
11
12
12
2
1
3
14

Acentrogobius audax
Acentogobius janthinopterus
Acentrogobius viridipunctatus
Amoya gracilis
Amoya moloana
Amoya raveni
Boleophthalmus boddarti
Cristatogobius rubripectoralis
Glossogobius celebius
Oxyurichthys ophthalmonema
Oxyurichthys tentacularis

L
M
N
O
P
Q
R
S
T
U

14
5
1
3
6
6
12
12
25
16

Periophthalmus argentilineatus
Periophthalmus gracilis
Periophthalmus malaccensis
Periophthalmus minutus
Periophthalmus novemradiatus
Pseudogobius javanicus
Sicyopterus cyanocephalus
Sicyopterus hageni
Sicyopterus microcephalus
Stiphodon elegans

Total

214

Morphometric data
Method of morphometric measurement followed Murdy (1989). The gobies
were measured using digital caliper with resolution of 0.01 mm. These study used
22 morphometric characters and their abbreviation were presented in Figure 2 and
Table 2. Measurement of all characters were expressed as a percent of Standard
Length (SL).

Figure 2 Morphometric characters of gobies.

8

Figure 2 Morphometric characters of gobies (continued).
Table 2 List of morphometric characters of gobies used in this study
NO

MORPHOMETRIC CHARACTERS

ABBREVIATION

Comparison with Standard length (SL)
1

Head length

2

Predorsal length
nd

HL
PrDL

3

Snout to 2 Dorsal Fin Length

SnD2f

4

Snout to ventral fin length

SnVf

5

Snout to anal fin length

SnAf

6

Caudal peduncle length

CpL

7

Caudal peduncle depth

CpD

8

st

D1b

nd

1 Dorsal Fin Base

9

2 Dorsal Fin Base

D2b

10

Anal fin base

Ab

11

Pectoral fin length

PfL

12

Ventral fin length

VfL

13

Body depth at ventral

BDV

14

Body depth at anal

BDA

15

Body width at anal

BWA

16

Ventral fin to anal

VfA

17

Snout length

SnL

18

Eye diameter

Ed

19

Check depth

CD

20

Postorbital length

POL

21

Head width at maximum

HDm

22

Head width at gill opening

HDgo

9

Meristic data
Methods of meristic count followed Murdy (1989). The first element of anal
and second dorsal fin may be a soft spine or a segmented ray. Anal and second
dorsal fin did not discriminate between spines and rays. The last two rays of each
fins were very close together and shared ultimate pterygiophore, so these rays
were counted as a single element (Springer 1978, 1983).
Scale count in logitudinal series (LSR) was begun from dorsoposterior
attachment of opercular membrane, continued on posteroventral diagonal to the
tip of the pectoral fin, and then in a straight line along the midline of the body to
the posterior edge of the hypural plate, determined externally. Transverse scale
count (TSR) was counted from anal fin origin dorsoanteriorly to the first dorsal
fin base. Predorsal scales (PSR) extended just anterior to the first dorsal spine.
These study used 8 meristic characters and their abbreviation were presented in
Figure 3 and Table 3.

Figure 3 Meristic characters (A) scale counts: LSR (red), TSR (yellow) and PSR
(blue). (B) Fin-ray count.

10

Table 3 List of meristic characters of gobies used in this study
No

MERISTIC CHARACTERS

ABBREVIATION

Fin-ray counts
1

First dorsal fin

D1

2

Second dorsal fin

D2

3

Anal fin

A

4

Pectoral fin

P

5

Segmented caudal fin rays

C

Scale counts
6

Longitudinal scale row

LSR

7

Transverse scale row

TSR

8

Predorsal scale row

PSR

Data Analysis
The morphometric measurements were standardized on Standard Length
(SL) to remove size effect (Lleonart et al. 2000). Morphometric data were log
transformed because the equation log (x/y) = log x – log y is a linear function of
log x and log y whereas x/y is not a linear function of x and y (Murdy 1989).
Principal Components Analaysis (PCA) was employed in multivariate comparison
using covariance matrix to eliminate the correlation between variables.
K-means clustering algorithm function was used to determine a prespecified
number of cluster centres to minimize the within-class sum of squares from those
centres (Venables & Ripley 1999). The analysis was followed by elbow criterion
method to estimate the best number of clusters. This methods used the ratio of
within-group to the total variance. The best number of clusters was estimated
when adding a group did not improve the explained variance (Claude 2008). The
closeness between clusters were estimated use Minimum Spanning Tree (MST)
(Xu & Wunsch II, 2009). Calculation was done using R 2.12.1.

CLUSTER ANALYSIS
Clustering of Gobies Based on Morphometric Characters
Mathematically 22 morphometric measurements build a character space
within which individual gobies floated. If the measurement values were same or
similar, they would cluster together. PCA was used to remove any correlation between
measurements, so the axes (Principal Components/ PCs) of the space were spanned
orthogonally.
In the character space, the true number of clusters is not known. So we used
elbow criterion method to determine the best number of clusters. Iteratively, adding a
number of clusters will add information (explain a proportion of variance) but at
some point the marginal gain will drop, giving an angle in the graph of number of
cluster versus variances (Twarakavi et al. 2010). Elbow criterion use the ratio of
within-cluster variance to total variance. The best number of clusters would be
estimated when adding a group did not improve the explained variance (Claude
2008). The number of clusters are chosen at this elbow (Twarakavi et al. 2010).
Iteration to cluster gobies was done using K-means method (Venables and
Ripley 1999). Table 4 suggested that the best number of clusters was seven because
adding a cluster did not increase the explained variance. These partition were showed
in principal-component space in Appendix 1. The best partition was showed in Figure
4.

Table 4 Percentage of variance explainable with adding number of clusters
Number of Clusters

Percentage of Explained Variance

2

28.41%

3

19.37%

4

12.19%

5

6.25%

6

5.8%

7

5.5%

8

1.61%

9

1.22%

Note : Partition of gobies into 8 and 9 clusters are not chosen because low of percentage of
explained variance

12

1.5

Seven Clusters

1.0

G
G G
G G
G G G
G
G

0.5

K
KK K
KK
J K
J KKKKK K
K

J

A

H
LL L
L
H P
L L
L
A
C
LL L
C C
L
C AC
B
BCC
P P
D
A
B BB C
AC
BBC
O R R
PE
DD D
B
B BC
O R
P
B
B
F
EF
C
FD
C
BB B B P C
D
E
F
C
C
RT
U MM
DD
FDD U
C
B
CDE E
ORR R
M
T
D
E
R
E
F
B
F
B C
U UR RT RTT
E
E F F FE UD
UM MR T
U
T TS
S
C

-0.5

0.0

C

PC2

G

G

Q

Q
Q

-1.5

-1.0

Q
Q

N

S
T
TT T
TS I S
TTS
T TS
S
T
T
S T
S
T
S S
T
T

UU
U UU
U
U
Q
U

-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

PC1

Figure 4 Plotting of all speciments in two first PC indicate centroid of clusters
and their minimum spanning tree
Figure 4 showed seven clusters of gobies based on morphometric data. This
clustering referred to genera level. They were Acentrogobius (B and C) as 1st
cluster, Amoya (D, E, and F) as 2nd cluster, Periophthalmus (L) as 3rd cluster,
Stiphodon (U) as 4th cluster, Sicyopterus (R, S, and T) as 5th cluster,
Boleophthalmus (G) as 6th cluster, and Oxyurichthys (K) as 7th cluster. The
closeness between clusters were estimated using Minimum Spanning Tree (MST),
which is defined as a tree with the minimal sum of the edge weights among all the
trees than contain all clusters (Xu & Wunsch II, 2009). The weight of the edge

13

between each pairs of clusters is the distance between those two clusters, where
the distance can be estimated using Euclidean distance method. Based on MST
result, the distance of 1st to 2nd cluster is 0.700; 2nd to 3rd cluster is 1.008; 2nd to 5th
cluster is 1.015; 2nd to 7th cluster is 1.064; 2nd to 4th cluster is 1.216; and 7th to 6th
cluster is 1.256.
Figure 4 is plotting specimens in principal component space using two
first PCs. Actually, the space has 22 PCs and each PC bear different sizes of
variance information. The first PC informed the higher score in eigen value
(0.3372) and this score contributed to 36.61% variation of data. The score of eigen
value in second PC was 0.2029 and the score contributed 22.03% variation of data
(Table 5).
Table 5 Eigen value, proportion of variance, and cumulative of variance.
PCs

Eigen
Value

Proportion of Cumulative
Variance (%)
(%)

PCs

Eigen
Value

Proportion of Cumulative
Variance (%)
(%)

1

0.3372

36.61

36.61

12

0.0084

0.91

96.95

2

0.2029

22.03

58.64

13

0.0060

0.65

97.61

3

0.1336

14.51

73.15

14

0.0052

0.57

98.18

4

0.0648

7.03

80.19

15

0.0036

0.40

98.58

5

0.0434

4.71

84.90

16

0.0035

0.38

98.96

6

0.0255

2.77

87.68

17

0.0025

0.28

99.24

7

0.0192

2.08

89.77

18

0.0022

0.24

99.49

8

0.0187

2.03

91.80

19

0.0019

0.20

99.69

9

0.0175

1.90

93.70

20

0.0012

0.13

99.83

10

0.0117

1.27

94.98

21

0.0009

0.10

99.93

11

0.0097

1.05

96.03

22

0.0005

0.06

100.00

Plotting of PC1 and PC2 account for 58.64% of cumulative variance.
Because the two PCs have more than half of total information, these PCs informed
high contribution of each characters in data separation. Tabel 6 showed eigen
vector score of each characters in PC1 and PC2. Six characters (SnVf, CpL, D2b,
Ab, VfL, and POL) have larger scores than others, so these characters should be
sufficient to be used as taxonomic character to separated gobies based on
morphometric data.

14

Table 6 Eigen vector of each character on first two PCs.
Characters

PC1

PC2

Characters

PC1

PC2

HL

-0.193

0.116

VfL

-0.389

0.194

PrDL

-0.073

-0.019

BDV

-0.222

0.093

SnD2f

-0.040

-0.041

BDA

-0.170

0.025

SnVf

-0.317

0.140

BWA

-0.016

-0.091

SnAf

-0.077

-0.020

VfA

0.162

-0.140

CpL

-0.167

-0.683

SnL

-0.005

0.092

CpD

-0.083

-0.211

Ed

-0.376

-0.032

D1b

-0.093

0.011

CD

-0.197

0.140

D2b

0.148

0.338

POL

-0.274

0.250

Ab

0.310

0.392

HDm

-0.282

0.133

PfL

-0.081

0.038

HDgo

-0.301

-0.023

Note: The bold characters showed higher score in cumulative variation of PC1 and PC2 than their
3rd quartile.

Clustering of Gobies Based on Meristic Characters
There are eight meristic characters (D1, D2, A, P, C, LSR, TSR, and PSR)
to clustering of gobies collected in the present study. Iteration to cluster was done
using K-means method and their result were showed in principal component space
(Appendix 2). Iteratively, adding a number of cluster will add explain a proportion
of variance and the best number of clusters would be estimated when adding a
group did not improve the explained variance. Based on this method, the best
number of gobies cluster used meristic count was seven (Table 7 and Figure 5).
Table 7 Percentage of variance explainable with adding number of clusters.
Number of Clusters

Percentage of Explained Variance

2

41.56%

3

19.10%

4

13.88%

5

9.00%

6

3.44%

7

2.95%

8

1.28%

9

1.22%

Note : Partition of gobies into 8 and 9 clusters are not chosen because low of percentage of
explained variance

15

1.0

1.5

Seven Clusters

L LL L
L LLLLLL
L LLO O

0.5

MM M M PPPP
P

0.0

CC
CC
C
CC
CC
C
C
RST T
CC
CC
C
R SR
RS
S
T T C
S
FCF
TS
S
RS
RRRRS
TTTTTTTTT
SR
E
B
B
UU
FF FE BB
B
B
B
U
RR TT T
B
UU
D FF
B
B
U
B
B
U
E
FDFE EEEB
T T TDDDD
B
U
UU
E
F
K
F
KK K T
B
D
U
D
D
E
T
U A
D
D
E
K
K
KK K
K K
T D
BE AA
T
ANA
K KJ J
H
K J

-0.5

PC2

I

O
M

QQ
QQ
QQ

H

-1.5

-1.0

GGG
GGG
GGG
G
G

-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

PC1

Figure 5 Plotting of all speciments in two first PC indicate centroid of clusters
and their minimum spanning tree
Figure 5 showed seven clusters of gobies based on meristic data. They were
G (1st cluster); L (2nd cluster); C (3rd cluster); D, F, and 8 of E (4th cluster); B, U,
and 3 of E (5th cluster); K and 10 of T (6th cluster); and R, S, and 15 of T (7th
cluster). Based on MST result, 4th cluster more close to 5th cluster than the other
clusters with distence 0.407; after that 6th to 7th cluster with distance 0.418; 4th to
6th cluster with distance 0.518; 3rd to 4th cluster with distance 0.663; 2nd to 7th
cluster with distance 0.968; and 7th to 1st cluster with distance 1.238.
Actually, these analysis has 8 PCs and each PC bear different sizes of
variance information. But we used two first PCs to plotting specimens (Figure 5)
because these PCs have more than half of total information of variance. The first

16

PC informed the higher score in eigen value (0.272) and this score contributed to
57.56% variation of data. Whereas, second PC informed 0.089 of eigen value
(18.84% variation of data). So plotting of PC1 and PC2 account for 76.40% of
cumulative variance (Table 8).
Table 8 Eigen value, proportion of variance, and cumulative of variance.
PC

Eigen Value

Proportion of Variance (%)

Cumulative (%)

1

0.272

57.56

57.56

2

0.089

18.84

76.40

3

0.054

11.37

87.77

4

0.034

7.19

94.97

5

0.012

2.51

97.49

6

0.006

1.16

98.65

7

0.004

0.90

99.56

8

0.002

0.44

100.00

Tabel 9 showed eigen vector score of each characters in PC1 and PC2.
These score informed high contribution of each characters in data separation Two
characters (LSR and PSR) have larger scores than others, so these characters
should be sufficient to be used as taxonomic character to separated gobies based
on meristic data.
Table 9 Eigen vector of each character on PC1 and PC2.
Characters

PC1

PC2

D1

-0.086

0.684

D2

-0.271

-0.343

A

-0.361

-0.389

P

-0.087

-0.279

C

-0.036

-0.113

LSR

-0.593

0.109

TSR

-0.488

-0.068

PSR

-0.436

0.395

Note: The bold characters showed higher score in cumulative variation of PC1 and PC2 than their
3rd quartile

IDENTIFICATION
Gobiidae are small fishes (up to 30 cm, usually less than 10 cm) with united
ventral fins, which are sometimes totally or posteriorly incised, basal membrane
present or absent. Two dorsal fins, separated or connected with their bases, sometimes
first dorsal fin absent. Body scaled with ctenoid or cycloid scales, sometimes partly or
totally naked. Gobiidae can be separated into five subfamilies, they are Amblyopinae
(worm-gobies), Gobiinae (true gobies), Gobionellinae (brackish-water gobies),
Oxudercinae (mudskippers), and Sicydiinae (freshwater gobies) (Koumans 1931;
Larson & Murdy 2001; Larson & Lim 2005).

Key to the subfamilies of Gobiidae from Lombok Island
1a. Lower jaw typically possessing only single row of teeth ................................2
1b. Lower jaw typically possessing more than 1 row of teeth ..............................3
2a. Pelvic frenum with fleshy lobes over spines (Fig. 6c); eyes lateral and without
eyelid (Fig. 7b) ................................................................................Sicydiinae
2b. Pelvic fins without frenum (Fig. 6a) or if frenum present without fleshy lobes
over spines (Fig. 6b); body elongate; eyes located mostly dorsally and with a
free lower eyelid (Fig. 7a) ..........................................................Oxudercinae
Ventral fins
without frenum

a

Fleshy lobes

No fleshy lobes

b

c

Figure 6 Ventral view of pelvic fins (a) Without frenum; (b) Frenum without
fleshy lobes; (c) Frenum with fleshy lobes

Eyes with eyelid

Without eyelid

a
b
Figure 7 (a) Ventral fins with frenum and fleshy lobes; (b) eyes lateral and
without eyelid
3a. Paired anterior interorbital pores and with a pore immediately behind anterior
nostril (Fig. 8a) ...........................................................................Gobionellinae
3b. A single anterior interorbital pore and without a pore immediately behind
anterior nostril (Fig. 8b) .....................................................................Gobiinae
Anterior nostril

Anterior interorbital
pore(s)

a

b

Figure 8 Head pores type (a) A pair and (b) A single of anterior interorbital pore(s)

Subfamily Gobiinae

Key to the genera and species of Gobiinae from Lombok Island
1a. Thin dermal crest on top of head anterior to first dorsal fin (Fig. 9); body
deep; second dorsal fin and anal fin with I spine and 9 soft rays (estuaries)
...................................................................................................Cristatogobius
(with a single species known in the area, Cristatogobius rubripectoralis)
1b. No dermal crest anterior to first dorsal fin .......................................................2

Dermal crest

Figure 9 Dermal crest on top of head.
2a. Tongue distinctly bilobed (Fig. 10) ..............................................Glossogobius
(with a single species known in the area, Glossogobius celebius)
2b. Tongue variable, usually rounded or concave ................................................3
Tongue distinctly
bilobed

Figure 10 Tongue distinctly bilobed.
3a. Opercles full scaled .............................................................Acentrogobius (4)
3b. Opercle naked ................................................................................. Amoya (6)
4a. Transverse papilla pattern on cheek ...............Acentrogobius viridipunctatus
4b. Longitudinal papilla pattern in cheek ........................................................... 5
5a. Anal spine rays I,8; the horizontal dark stripes across the cheek and pectoral
base ................................................................Acentrogobius janthinopterus
5b. Anal spine rays I,9; dark bar on caudal peduncle and caudal base ..............
.........................................................................................Acentrogobius audax
6a. Total D2 elements usualy I,10; LSR less than 40 (usually 30-36) ...................
................................................................................................Amoya moloana
6b. Total D2 elements usualy I,11; LSR more than 40 (usually 39-48) ..............7
7a. First dorsal fin with filamentous extension ...............................Amoya raveni
7b. First dorsal fin without filamentous extension ........................Amoya gracilis

Genus Acentrogobius Bleeker
Acentrogobius audax (Smith, 1959)

Figure 11 Acentrogobius audax, 43.33 mm in SL, Selindungan, Sekotong districwestern Lombok.
Material Examined
Five specimens from Selindungan, Sekotong. Size ranges are 29.94 to 43.33 mm
in SL.

Diagnosis:
D. VI; I,9-10; A. I,9; P. 16-17; longitudinal scales 27-29; transverse scales 8;
predors